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PROTEIN DATA BANK QUARTERLY NEWSLETTER
Release #83 - January 1998
Published by
Brookhaven National Laboratory
Protein Data Bank
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
Internet Sites
WWW http://www.pdb.bnl.gov
FTP ftp.pdb.bnl.gov
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January 1998 CD-ROM Release
6947 Released Atomic Coordinate Entries
Molecule Type
6151 proteins, peptides, and viruses
268 protein/nucleic acid complexes
516 nucleic acids
12 carbohydrates
Experimental Technique
168 theoretical modeling
1089 NMR
5690 diffraction and other
1673 Structure Factor Files
400 NMR Restraint Files
The total size of the atomic coordinate entry
database is 3.0 GB uncompressed.
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Table of Contents
What's New at the PDB
Archive Management
EBI Now Accepting AutoDep Submissions
The `Intelligent' Search Engine Behind the 3DB Browser(TM)
Request for a Revision of IUCr Policy on Publication
and Deposition of Crstallographic Data
PDB Computer Services
Energy Department Announces New BNL Contractor
Exceptional Science Fair Project Uses the PDB
Writing Structure Factors in mmCIF using CCP4
Protein Topology WWW Site
SARF2 - a Program for Comparison of Protein Structures
Molecular Docking by Fourier Correlation with FTDOCK
MolView and MolView Lite
OLDERADO: Extracting Single Structures, Core Atoms
and Domains from a NMR-derived Ensemble
Notes of a Protein Crystallographer-
FRODO, the Electronic Hobbit
Web Sites Referenced in the January 1998
PDB Newsletter
Affiliated Centers and Mirror Sites
Related WWW Sites
PDB(TM) Order Form
PDB Access, FTP Directory Structure,
Consultants, Staff, Support and Instructions to Authors
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What's New at the PDB
Joel L. Sussman
Structure factors are the observed experimental data from X-ray crystallographic
experiments. They are the basis of the X-ray coordinate entries and as such
need to be readily available to and usable by researchers. To facilitate the
exchange of this data between scientists, as well as for their deposition and
retrieval from the PDB, it was decided to set up a standard format, i.e., a
Lingua Franca, for structure factors.
The PDB and a number of macromolecular crystallographers, including the
Chairperson of the IUCr Working Group on Macromolecular CIF, Dr. Paula
Fitzgerald, and other members of this committee, developed a standard
interchange format for structure factors. This standard is in mmCIF format,
i.e., the IUCr-developed `macromolecular Crystallographic Information File'. It
was chosen for simplicity of design and for being clearly self-defining. The
format is also easy to extend, by simply adding additional tokens as new
crystallographic experimental methods or concepts are developed (see the
January, 1996 PDB Newsletter and
ftp://ftp.pdb.bnl.gov/structure_factors/cifSF_dictionary). The entire mmCIF
crystallographic dictionary has recently been ratified by the IUCr's COMCIFS
committee (http://ndb.rutgers.edu/NDB/mmcif/).
We have been strongly urging our depositors to submit structure factors with
their entries (Baker et al., 1996). We are pleased to report that since the
release of the PDB's Web-based deposition tool, AutoDep, in October 1996, that
almost two-thirds of the depositions of X-ray structures to the PDB are now
accompanied by their structure factors. Dr. Jiansheng Jiang, at the PDB, has
converted these recently-deposited structure factors, as well as virtually all
the previously-deposited ones, to the standard mmCIF format. The structure
factors are available through the PDB's Web-based 3DB Browser(TM)
(http://www.pdb.bnl.gov/pdb-bin/pdbmain), as can be seen on the Browser's
`Atlas' page for each structure.
Over the years, the PDB has observed that one of the most useful reasons for
storing structure factors is for the crystallographer who did the experiment to
be able to retrieve his/her own data which have been misplaced in their
laboratory. In parallel, the fact that this data is now easily available, and
in a standard format, has already begun to foster new community-wide efforts at
improvements in validation techniques based on the experimental data, e.g.,
SFCHECK by Vagin, Richelle & Wodak (http://www.sdsc.edu/Xtal/IUCr/CC/School96/),
the Uppsala Electron Density Server by Taylor
(http://alpha2.bmc.uu.se/valid/density/form1.html), and others.
References:
Baker, E. N., Blundell, T. L., Vijayan, M., Dodson, E., Dodson, G., Gilliland,
G. I. & Sussman, J. L. (1996). Crystallographic Data Deposition. Nature 379,
202.
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Archive Management
Enrique E. Abola
Layered Release
In the October 1997 PDB Quarterly Newsletter, we discussed the layered-release
that will allow for a virtually immediate release of entries (to be referred to
as the 1st layer) without staff intervention. A PDB ID code will be issued only
after the depositor gives approval to release his/her entry either immediately
or as soon as it comes off hold. Following this, PDB staff will process the
entry as done presently. This processing will include standardization of
nomenclature, other annotation, and more importantly, data representation. Most
of this work covers issues not now fully delegated to software. The resulting
entry will be loaded on our servers as the 2nd layer. The set of mandatory items
to be required before data are accepted was discussed in the October 1997 PDB
Newsletter. The complete list may be found at our Web site
(http://www.pdb.bnl.gov).
Listed below are a series of checks that will be done on an entry as part of the
submission process. The first checks will be used to ensure that entries with
obvious deficiencies are not released (e.g., duplicate atom records). The other
checks will be used to add annotations to the entry. When the coordinates are
loaded on the PDB server, a file containing the results of the diagnostic runs
will be loaded as well.
The following tests will be done on the entry as part of the submission process.
Results of the tests will be provided to the depositor who can then take the
appropriate action given the options outlined below before a PDB ID is issued.
1. Diagnostics requiring corrections and re-submission of coordinate data.
* More than one polypeptide or nucleotide chain assigned the same chain name
* Heterogen group specified by HET and FORMUL records not present in the
ATOM/HETATM records
* More than 10% of the atoms involved in unusually close crystal packing
interactions (this check will also cover the case for which a non-standard
space group setting was used and the correct set of symmetry operators were
not provided)
* Violation of atom nomenclature for standard amino and nucleic acids
* Duplicate ATOM or HETATM records in the same residue with the same atom name
or the same coordinates
* ATOM/HETATM records not correctly formatted
* Heterogen ID provided in the coordinate file conflicts with the PDB Het
Dictionary
2. Diagnostics requiring annotations and/or comments to be provided by the
depositors if the data are not corrected. The PDB will insert a CAVEAT record
before release.
* For polypeptides, phi-psi angles for more than 20% of the residues outside
the allowable region
* Unexpected chirality at C-alpha center
3. The following diagnostics are normally used by PDB staff to take a
closer look at the data because, by experience, we have found that they may be
indicative of unusual structures or possible problems. We will present this
information to the depositor and the list will also be included in a file
containing the output of our checking runs to be made available to the users.
The depositor may, of course, modify the coordinate file during the submission
process to correct for possible errors before giving final approval to release
the data.
* RMSD of bond lengths greater than 0.08 Angstroms from ideal values
* RMSD of bond angles greater than 5.0 degrees
* Breaks in the chain (e.g., due to disorder)
* Differences between amino acid sequences given by the ATOM records and those
given in the appropriate sequence database entry
* Amino acid sequences not reported in any sequence database
* CIS-peptides and peptide bonds that deviate significantly from the expected
trans conformation
* Individual bond lengths differing by more than 0.1 Angstroms from standard
values
* Individual bond angles differing by more than 15 degrees from standard
values
* Atoms too close to symmetry axes
* Atoms involved in unusually close crystal packing interaction
* Atom occupancies less than or equal to 0.0 or occupancies greater than 1.0
* Atom occupancies less than 1.0 and for which no alternate location ATOM
record is provided
* Missing residues, missing atoms
* Thermal factors greater than 100 A**2
* Unexpected deviations from planarity
* Non-standard SCALE matrix
* OXT atom record in the middle of a chain (flagged as extra atom), typically
occurring before a gap in the coordinates
* R value greater than 30%
* Free-R value greater than 35%
* Free-R and R value differ by more than 10%
* RMSD between atoms related by NCS MTRIX records is greater than 3.0
Angstroms
Tests which are valid only for diffraction experiments will not be applied to
entries reporting NMR experiments or model building studies.
Heterogen groups will be checked against the current PDB Het Dictionary. The
only check that will be done at this stage of the processing is to see if the
HET ID and the atom nomenclature used for a group is consistent with the
dictionary (e.g., is the GLC group in the coordinate file a glucose molecule as
given in the PDB Het Dictionary and are the atoms properly named?). Groups that
are not in the dictionary and for which there is no conflict on the HET ID code
will be accepted as is and will be checked and standardized as part of the
regular processing to be done after the first layer is loaded.
Complete descriptions of these tests along with a more precise definition of
values such as those defining allowable Ramachandran plot regions are provided
on our Web pages (http://www.pdb.bnl.gov). Please send your comments and
suggestions regarding these tests and/or on the layered-release to
abola1@bnl.gov.
Summary of Data Processing Activities for 1997
In 1997 we received 1,844 coordinate sets and released 1,631. This averages out
to 153 entries deposited per month which is about 27% more than the 1996
submission rate. On average it took us 119 days to release an entry, which is
significantly improved from the 173 days that it took us to release an entry in
1996. A plot giving the growth in data deposition as well as the turn-around
time is provided on the back cover of this Newsletter. The plot is accessible
via our Web Home Page, and is updated after every load.
There were several changes in our procedures that have allowed us to handle the
increased rate of deposition while at the same time reducing the amount of time
required for processing. Most significant was the release of our AutoDep program
in October 1996 that has greatly simplified processing of entries. More than 70%
of the entries submitted in 1997 were done through AutoDep.
Starting in November 1997 we initiated a new procedure in which entries are
released every Tuesday night. This was done at the request of several Mirror
Sites, most of which have programs that automatically generate indices relating
PDB entries to other databases. Users wishing to check data loads can visit our
Home Page for a list of recently released ID codes.
--------------------------------------------------------------------------
EBI Now Accepting AutoDep Submissions
The following announcement was posted on several listservers and newsgroups on
December 23, 1997, including the PDB Listserver, X-PLOR Listserver, and the O
Listserver.
Deposition of 3D Structural Studies of Biological Macromolecules
We are pleased to announce the inauguration of a new deposition site for 3D
structural studies of biological macromolecules. Starting on January 5, 1998,
authors using the Web-based tool, AutoDep, can submit data either to the
European Bioinformatics Institute (EBI), UK or to the Protein Data Bank (PDB) at
Brookhaven National Laboratory (BNL), USA. The additional site is expected to
significantly facilitate the submission procedure, especially for European
researchers.
AutoDep is a Web-based tool originally designed at PDB for automatic submission
of macromolecular data into the PDB. Extensive collaboration between EBI and
PDB has produced significant changes to the original system allowing for the
seamless operation of multiple deposition sites. This includes EBI
specifications for standards and protocols to be used in making the code
portable and generally more robust.
AutoDep is accessible from the following URLs:
* BNL-PDB http://www.pdb.bnl.gov
* EBI-MSD http://autodep.ebi.ac.uk
Those wishing to submit data using the electronic version of the Deposition Form
must continue to deposit directly to BNL using e-mail or FTP.
The submission procedure will be identical, and equivalent, at both sites, but
PDB ID codes will be issued by BNL. Data submitted at EBI will be forwarded
automatically to PDB after depositors have reviewed the AutoDep-generated entry
and diagnostics. Final preparation for archiving and release will be done by
PDB staff. We encourage depositors to submit not only the structural results,
but also their experimental data, i.e., for crystallographers, X-ray structure
factors, and for NMR spectroscopists, constraints lists and statistical data
describing the calculated NMR conformers and constraints.
Important Notes:
(i) Submissions can be completed only at the site at which they were started.
(ii) The option "Based on a previous submission" may be used to simplify
submissions by using an earlier AutoDep session as a template. However,
depositors will only have access to their earlier submissions at the site
where those submissions were originally made.
(iii) Existing PDB entries may be used as templates by choosing the option
"Based on an existing PDB entry". The full set of entries will be available
at either site, irrespective of where the original deposition was made.
(iv) The date of submission for data deposited at EBI will be the corresponding
U.S. Eastern Time of the date when submission is completed at EBI.
(v) EBI staff will offer assistance (via e-mail: pdbhelp@ebi.ac.uk) up to the
point of submission. Once BNL has issued an ID code, correspondence should be
directed to BNL (via e-mail: pdbhelp@pdb.bnl.gov).
Please note that authors should continue to deposit crystal structures of
nucleic acids to the Nucleic Acid Database (NDB) at Rutgers, the State
University of New Jersey, USA at URL:
http://ndbserver.rutgers.edu:80/NDB/deposition/index.html.
Experimental data related to NMR studies will also be transferred electronically
to the BioMagResBank (BMRB) at the University of Wisconsin-Madison, USA for
further processing and inclusion into the database (http://www.bmrb.wisc.edu) as
well.
Joel L. Sussman Phil McNeil
Head, Protein Data Bank Head, Macromolecular
Biology Department Structure Group
Brookhaven National Laboratory EMBL Outstation
Upton, NY, USA European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
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The `Intelligent' Search Engine Behind the 3DB Browser(TM)
Jaime Prilusky
Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel
(lsprilus@weizmann.weizmann.ac.il)
The new 3DB Browser(TM) allows the user to rapidly search through the contents of
the entire PDB Archive for entries matching certain constraints. A full text
search can be made for any string appearing in the text of a PDB entry,
excluding the coordinate records. Many specific records can be searched for
regular expressions or numerical limits. 3DB Browser gives you the option of
saving object sets resulting from queries. This saved set can be used as a
starting point for further database operations or as a reference for your work.
Every saved set includes the date of the search and the query from which it was
generated.
The Search Fields of the 3DB Browser
The main source of information for the 3DB Browser is the data from the Protein
Data Bank. This data is highly structured and most of the crystallographers are
used to thinking of a piece of data from a PDB entry as belonging to a
particular "record" or "field". It makes sense to use these fields to constrain
the search. Searching for `rich' as a keyword has a different meaning than
searching for the author Rich.
Search Field PDB Entry
PDB ID code Four-character accession code
Keyword Molecule name, class or family, or related term (HEADER,
TITLE, KEYWDS and COMPND fields)
Author Family name of depositor or author of associated publication
(AUTHOR and JRNL fields)
Text query Any word in the complete PDB text, excluding the field names
FASTA Search Fasta search of the sequence
Experiment Method of structure determination
Resolution A unique value or range of values, in Angstroms (REMARK 2
field)
Space group Both extended and standard Hermann-Mauguin symbols (CRYST1
field)
Organism Trivial name, systematic name or expression system (SOURCE
field)
Date (lower) Date entry was released or updated
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Associated group Prosthetic group, metal ion, ligand or substrate, or its three
letter PDB abbreviation (HET and HETNAM fields)
Examples and Boolean-style Searches
The simplest operation with the browser is to enter one or more words in the
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The symbol `*' can be used as a wild card, to denote a sequence of any number
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The Boolean operator AND is the default for 3DB Browser, and mandatory (you
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Inside a given field, you may apply Boolean logical operators at will to the
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The case is unimportant. The operator AND can be represented by `+' and the
operator NOT represented by `-'.
For example, `zinc and (torpedo or snake)' in the Text query field will return
those entries that contain either the word torpedo or the word snake, but only
where the word zinc is also present.
To Err is Human
One of the main concerns for us, as database-interface developers, is the "false
negatives", that is, to not return data after a query, even when the data are
available in the database. Frequently this happens because the user was unable
to express the query in a way compatible with the search engine, or used words
or keywords unknown to the search engine.
3DB Browser deals with this problem by incorporating several automatic and semi-
automatic mechanisms to help the user in retrieving the requested data. The
request from the user gets filtered and transformed by one or more of the
following engines. At the end, the resulting query is the one used for the
search.
Engine Example
american-british `amoeba' and `ameba' are equivalent
synonyms `protease' is equivalent to `proteinase'
spelling search based on a dictionary built from the current PDB data, the
spelling engine will produce words that are close to the
entered one. As an example, entering `imune' will offer
`immune' as a valid alternative.
soundex search based on the soundex algorithm that approximates the sound of
the word when spoken by an English speaker. Looking for
author `weich' will offer as alternatives: Weiss, Wess,
Wyss ...
Inside this section on understanding what the user looks for, we can include the
improved search on the CRYST1 record using the short and extended Hermann-
Mauguin symbols. You may enter either `P 1 21 1' or `P 21' in the Space group
field and get the same result.
3DB is Just the Starting Point
A search in 3DB brings up a rich Atlas page summarizing additional knowledge
related to the entry of interest. The links in this Atlas page carry you to the
original sources of information. The number of external sources that 3DB
searches and dynamically incorporates into the Atlas pages increases daily. The
following table summarizes the external sources currently referenced by 3DB.
Source Name Short Description
BioMagResBank Relational Database for Sequence-Specific Protein NMR Data
BLOCKS Database of conserved regions in groups of proteins
CATH Protein Structure Classification
Dali/FSSP Families of Structurally Similar Proteins
EMBL European Molecular Biology Laboratory
Entrez NCBI's Documentation database
ENZYME Enzyme nomenclature database
ESTHER ESTerases and alpha/beta Hydrolase Enzymes and Relatives
GenBank NIH genetic sequence database
GDB Genome Data Base
Kinase Protein Kinase Database Project
KineMage Protein Science's Kinemage server
LPFC Library of Protein Family Cores
MacroMolecule EBI's Crystal MacroMolecule Files
MMDB Molecular Modelling Database
NBD Nucleic Acid Database
OLDERADO Core, Domain and Representative Structure Database
PDBOBS Archive of obsolete PDB entries at SDSC
PDBREPORT Structure verification reports for X-ray structures
PIR Protein Information Resource
PROSITE Dictionary of protein sites and patterns
ProtMotDB Protein Motions Database
scop Structural Classification of Proteins
SWISS-3DIMAGE 3D images of proteins and other biological macromolecules
SWISS-PROT Annotated protein sequence database
TREMBL TRanslation from EMBL
If you know of other sources of information related to PDB that can be
incorporated into 3DB's Atlas page, please send an e-mail message to
lsprilus@weizmann.weizmann.ac.il.
Support your Local Store
The Protein Data Bank has several mirror sites across the world. These sites
have the same data and facilities as in the central PDB server. They are just
closer to you, and, frequently, faster to access on the Internet. To help you
know your neighborhood, the 3DB Browser incorporates "closer-site", an automatic
script that detects your location and offers alternative sites that are closer
to you (in the network sense).
Drop an e-mail to lsprilus@weizmann.weizmann.ac.il if you are interested in
getting the "closer-site" script for your own application.
--------------------------------------------------------------------------
Request for a Revision of IUCr Policy on Publication and Deposition of
Crystallographic Data
Alex Wlodawer
Macromolecular Structure Laboratory, ABL-Basic Research Program, Frederick
Cancer Research and Development Center, National Cancer Institute, Frederick,
MD, USA (wlodawer@ncifcrf.gov)
Dear Colleagues,
For the last two years, I have been working on trying to change the policies of
journals and funding agencies which allow hold periods of up to one year for the
coordinates resulting from crystallographic and NMR studies. (See also Sussman
1997.) It is now becoming clear that the best way to accomplish such a change
would be to induce IUCr to change their official recommendations (International
Union of Crystallography, 1989). Several of us have recently written a letter
to Science, which appeared in the January 16th issue (Wlodawer, 1998),
suggesting that their policy be modified. It is necessary, however, to involve
the largest possible segment of the structural community in this endeavor. For
that purpose, we are circulating a petition which will be presented to IUCr. If
you agree with the text of the petition below, please send a brief message to me
at the e-mail address wlodawer@ncifcrf.gov. You might also wish to send a
message if you disagree with the petition and would like to keep the current
policy in place. The results of this vote will be reported to the community
before any further action is taken.
References:
International Union of Crystallography. Commission on Biological Macromolecules.
(1989) Policy on publication and the deposition of data from crystallographic
studies of biological macromolecules. Acta Crystallogr., Sect.A, 45, 658.
(Policy also in section 11.3 of http://hobbes.gh.wits.ac.za/iucr-
top/journals/acta/actaa_notes.html).
Sussman, J. L. (1997) What's new at the PDB. PDB Q. Newsl., No.82, 1.
Wlodawer, A., Davies, D., Petsko, G., Rossmann, M., Olson, A. & Sussman, J. L.
(1998) Immediate release of crystallographic data: a proposal. Science, 279,
306.
Petition:
To: Commission on Biological Macromolecules, IUCr
We, the undersigned, would like to request a revision of the IUCr policy on
publication and deposition of data from crystallographic studies of biological
macromolecules (Acta Cryst. A45, 658 (1989). It is our intention that if the
policy gets revised, the new rules will be communicated to granting agencies and
to scientific journals, in order to be universally accepted.
The current policy has been implemented on the basis of the discussions which
had taken place a decade ago. In the meantime, there has been an incredibly
rapid increase in the rate of determination of 3D structures of
biomacromolecules, as reflected by the deposition of a new structure in the
Protein Data Bank (PDB), on average, every five hours. Unfortunately, in
parallel, an increasing proportion of depositors take advantage of the PDB's
policy of allowing structures to be kept `on hold' for up to a year after
coordinate deposition. Consequently, as many as 45% of newly deposited
structures are not available when the relevant papers are published.
When the issue of deposition was debated by the community ten years ago, the
time needed to solve a macromolecular structure was often measured in years, and
was rarely less than one year. The time needed for detailed analysis of such
structures was also fairly long. The one-year hold on coordinates was therefore
instituted to allow the authors to reap the fruit of their tremendous investment
of time and effort. Due to recent advances in protein expression and
purification, crystallization procedures, X-ray instrumentation, and computer
software, the time needed to solve a structure is often shorter than the allowed
hold period. In light of such developments, it is very difficult to justify
withholding coordinates for any period once the paper has been published.
Biomolecular structure analysis has indeed succeeded in bringing 3D structures
to the forefront of molecular biological research. This success has expanded
both the interest in and utility of the information being deposited in the PDB.
The molecular modeling community has grown and evolved considerably due to the
expansion of this source of experimental data. The value of the data rests in
their availability to the broader community. Methods are continuously being
developed to analyze new structures and their relationships to the collection of
existing structures. New uses for these data, such as statistical potentials
for folding and threading calculations, and interface recognition tools, are
evolving rapidly. No single research group can fully exhaust this wealth of
information. The value of the resource grows proportionally to the timeliness
of the data and to the number of scientists who have access to them. 3D
structural information is also a crucial link elucidating the role of a
translated region of a DNA sequence of unknown function.
We feel most strongly that the time has come to change the rules of deposition
so as to ensure that the coordinates are released concomitantly with publication
of the paper(s) describing the structure. We are convinced that without access
to the coordinates, the structures cannot be utilized for comparison with other
proteins, for theoretical analysis or, more and more importantly, for drug
design. We propose that coordinates deposited at the PDB should be marked as
either "for immediate release" or "to be released upon publication". We also
recommend that the maximum hold for primary data, i.e., X-ray structure factors,
and NMR-based restraints, be reduced from 4 years to 1 year. These changes would
bring macromolecular crystallography into line with the requirements of other
fields, such as gene sequencing, which have never allowed extended hold periods.
--------------------------------------------------------------------------
PDB Computer Services
John McCarthy
PDB's WWW Browser Discontinued
During the final six months of 1997, usage of the PDB's WWW Browser had dropped
significantly. Additionally, in December of 1997 the PDB released the latest
version of the 3DB Browser(TM). It has all the features of the WWW Browser plus
many more (see "The `Intelligent' Search Engine Behind the 3DB Browser(TM)" in
this Newsletter). For these reasons, the PDB discontinued the WWW Browser in
December of 1997. Please remove any bookmarks to it that you might still have.
PDB CD-ROM Files Compression
As was reported in the July 1997 PDB Quarterly Newsletter, the PDB started
compressing files on its October 1997 CD-ROM release. The Structure Factor
files were compressed allowing the full CD-ROM release to fit on six CDs.
The January 1998 CD-ROM release, most likely, will still fit on six CDs by
compressing the Structure Factor files, but in the near future, coordinate entry
files will be compressed as well.
As was stated in the July 1997 PDB Newsletter, an effect of compression will be
that the filenames will be different. Files that had the PDB ".ent" suffix will
have the ".gz" suffix when compressed. Any scripts that read coordinate entry
files directly from the CD-ROM will have to be modified to use the new filenames
and perform the uncompression as necessary. The PC-based browser PDB-Shell has
been updated to be able to read compressed entry files.
The PDB is using the Gnu gzip package to perform the compression and is
distributing the Gnu Gunzip package in the CD-ROM set to allow CD-ROM users to
perform uncompression.
A questionnaire was sent to all users receiving the July 1997 CD-ROM release
requesting their views regarding compression of files on the CD-ROM release.
The responses were overwhelmingly in favor of compression.
--------------------------------------------------------------------------
Energy Department Announces New BNL Contractor
Based on Department of Energy press releases
(http://apollo.osti.gov/doe/whatsnew/pressrel/pr97130.html and
http://apollo.osti.gov/doe/whatsnew/pressrel/pr98001.html)
Completing a major step in its ongoing effort to improve management and restore
confidence at Brookhaven National Laboratory, the Department of Energy announced
on November 25, 1997, the selection of Brookhaven Science Associates (BSA) as
the new contractor to manage and operate its Long Island, NY, research facility.
The BSA team is led by the Research Foundation of the State University of New
York on behalf of the State University of New York at Stony Brook and Battelle
Memorial Research Institute of Columbus, Ohio.
Secretary of Energy Federico Pena said, "Brookhaven Science Associates has
demonstrated leadership at their institutions, and I will look to them to fully
integrate safety and environmental protection into scientific research, to
accelerate and intensify recent efforts to rebuild community trust, and to
achieve overall excellence. Working together, we will make it possible for the
laboratory to carry out its mission as a world-class research facility and prove
itself a good neighbor to Suffolk County and Long Island."
"This is the fastest competition we have ever held for a management and
operating contract, and reflects a new way of doing business at the Department
of Energy," he added.
Two proposals from nonprofit-led teams were submitted in response to a July 18,
1997, Request for Proposals. One proposal was from BSA. The other competing
team was led by the IIT Research Institute of Chicago, Illinois. Both teams
provided excellent proposals and demonstrated their ability to manage
scientific, environmental, safety and health, and community involvement
initiatives at the laboratory. The selected team demonstrated the best total
capability to improve the laboratory's performance.
Stony Brook is a national leader in high energy and nuclear physics. Battelle
Memorial Research Institute has operated the department's Pacific Northwest
National Laboratory in Richland, Washington, for the last 32 years and has long
been a leader in applied science and technology, including environmental, safety
and health management. Battelle manages environmental, safety and health
activities at the department's Pantex Plant.
BSA committed to exceeding the requirements of the department's Request for
Proposal in several areas, including: the department's safety management program
that integrates safety into employees' daily work activities; implementing IS0
14001, an international standard for environmental management systems; and
instituting a Voluntary Protection Program whereby the lab will subscribe to
meeting proven industrial standards for worker safety.
Other immediate organizational commitments include retention of existing salary,
benefits and tenure systems for employees and appointment of separate deputy
directors for science and operations. In addition, offices for environment,
safety and health, environmental management, reactor operations and community
involvement will report directly to the laboratory director.
The BSA proposal identified Dr. John Marburger as the new Brookhaven Laboratory
director. Dr. Marburger is a distinguished science administrator and served as
State University of New York at Stony Brook's president for 14 years. He has
committed to integrate laboratory safety with scientific excellence and to
regain community trust and confidence.
The department's streamlined process for selecting a new contractor, limited to
nonprofit organizations or teams led by nonprofit organizations, was completed
in six months, rather than the usual 18, and was developed with extensive
community, industrial and academic involvement. The department initially
planned to award the contract in mid-November 1997. However, the award was not
signed until January 5, 1998, in order to comply with recently enacted federal
legislation requiring 60-day notice to the United States Congress before
awarding certain contracts.
BSA will assume responsibility for laboratory operations following a transition
period of 55 days after the contract award. Until that time, Associated
Universities Inc., the current contractor for Brookhaven, will continue to
manage the laboratory.
An introduction to BSA is available at: http://www.pubaf.bnl.gov/pr/BSA.htm.
The source selection statement is available at: http://www.ch.doe.gov/bnlseb.
--------------------------------------------------------------------------
Exceptional Science Fair Project Uses the PDB
Reprinted below is a letter from a father about his son's use of the PDB.
The PDB entry used was 1FKS: FK506 AND RAPAMYCIN-BINDING PROTEIN (FKBP12). The
molecular dynamics program referred to was PMD, Parallel Molecular Dynamics
(http://tincan.bioc.columbia.edu/pmd/pmd-summary.html), written by Dr. Andreas
Windemuth.
25 Nov 1997
Hello Dr. Sussman,
I was at the SuperComputing 97 show last week in San Jose, CA, and I stopped
by the Brookhaven National Laboratory booth. I talked about my son who did his
high school science fair project last year using the PDB at BNL, and the folks
in the booth strongly suggested that I write you a short note describing his
work.
My son had a kidney transplant and one result of this is that he takes
immunosupressive drugs to prevent organ rejection. While searching the PDB, he
found a few entries that were the binding proteins for a commonly used
immunosupressive. He copied the structure from the PDB server and then ran the
structure through a molecular dynamics program available from Columbia
University to generate the full 3D structure of the protein. He experimented
with the protein by making single atom changes in one of the 107 amino acids,
and had the MD program recompute the structure. He then compared the resulting
shape of the new protein to the original protein to estimate the ability of his
new protein to bind to the immunosupressive drug. He found that there were
several changes he could make to the protein that would appear to have little
impact on its binding capabilities, while other simple one-atom changes resulted
in a very different 3D structure. He was able to conclude, based upon residual
displacements and by using RasMol to visualize the structures, which proteins
would still be active in binding to the immunosupressive and which would not.
His science fair project was well received at both his school, Marian High
School in Framingham, MA, as well as at the regional science fair at Worcester
Polytechnic Institute and at the Massachusetts state science fair at MIT.
This was a wonderfully educational experience for him, and gave him a positive
experience in rational drug design. The relevance of this type of science to
his daily life was made quite clear to him. The educational capabilities of
having this type of data available on the Internet should not be overlooked.
Regards,
Dr. Don Dossa
Digital Equipment Corp
The entire PDB sends best wishes to Dr. Dossa's son for good health in the
future.
--------------------------------------------------------------------------
Writing Structure Factors in mmCIF using CCP4
Peter Keller
European Bioinformatics Institute, Hinxton Hall, Cambridge, CB10 1SD, UK
(keller@ebi.ac.uk)
Depositing your MTZ-formatted structure factor data to the PDB using the Web-
based AutoDep procedure is quite straightforward: all you need to do is use the
`CIF' output option of the CCP4 program `mtz2various'. The output file can then
be uploaded along with your coordinate file, when you start your submission.
The PDB strongly encourages use of this procedure to prepare your structure
factor file for submission.
Unlike the other output formats of mtz2various, the mmCIF output will contain
every reflection which is present in the MTZ file, even if the structure factor
amplitude is the missing number flag, or the reflection is systematically absent
for the space group which was finally assigned to the data. Each reflection is
flagged in the output according to its status (see the CCP4 documentation on
mtz2various for more information).
Other ways to indicate the status of reflections in the output file:
* The `FREEVAL' option can be used to indicate the test set that was excluded
from refinement for calculation of the free R factor.
* If, for some reason or other, you have performed your final refinement against
a subset of the data, you can indicate the resolution limits with the `RESO'
option, and a sigma cutoff with
`EXCLUDE SIGP'.
A simple example might look like this:
mtz2various hklin sf.mtz hklout sf.cif
OUTPUT CIF data_sf
LABI FP=FNAT SIGFP=SIGFNAT
END
A more complicated example:
mtz2various hklin sf.mtz hklout sf.cif
OUTPUT CIF data_sf
LABI FP=FNAT SIGFP=SIGFNAT I(+)=INAT SIGI(+)=
SIGINAT FREE=FREEFLAG
FREEVAL 2
RESO 15.0 2.1
END
In this case, the reflections for which the FREESET column is 2, have been used
as the free R test set, and only data between 15 and 2.1 Angstroms were used in
the refinement. Also, the merged intensities which were input to `truncate' have
been retained in the data file, and are being written to the output mmCIF.
The parameter following `OUTPUT CIF' must begin with `data_'. The characters
which follow identify the data, and are to some extent arbitrary: they will be
changed by PDB staff as appropriate when your submission is processed. If you
are unsure what to put here, choose some alphanumeric string which means
something to you, such as the MTZ filename or the name of the protein.
The name of the original MTZ file appears within the first few lines of the
output file - look for `_audit.creation_method'.
Anomalous data are handled with the DP/SIGDP (and I(-)/SIGI(-)) column
assignments.
--------------------------------------------------------------------------
Protein Topology WWW Site
David R. Westhead1,4, Daniel C. Hatton1 and Janet M. Thornton1,2,3
1 European Bioinformatics Institute, EMBL outstation, Wellcome Trust Genome
Campus, Hinxton, Cambridge, CM10 1SD, UK
2 Biomolecular Structure and Modelling Unit, Department of Biochemistry and
Molecular Biology, University College, London, WC1E 6BT, UK
3 Laboratory of Molecular Biology, Department of Crystallography, Birkbeck
College, University of London, Malet Street, London, WC1E 7HX, UK
4 E-mail: westhead@ebi.ac.uk
We have recently set up a WWW site (http://tops.ebi.ac.uk/tops) devoted to
protein structural topology. The central service offered at this site is an
"atlas" of protein topology cartoons in which each PDB entry has a
representative topology cartoon. Also available is a "server" facility to which
protein structures can be submitted (in PDB file format) for cartoon
calculation, and a good deal of information about protein structural topology.
Protein topology cartoons are simple two-dimensional schematic diagrams of
protein folds. They represent a fold as a sequence of secondary structure
elements (helices and strands) and show the relative position and direction of
these elements in the fold. An example cartoon is shown in figure 1. Protein
three-dimensional folds can be complicated and difficult to interpret. The aim
of topology cartoons is to simplify them so that they can be more easily
understood and compared. The simplification afforded by the cartoon in figure 1
is clear.
[figure not available as text]
Figure 1. The topology cartoon and 3D structure of superoxide dismutase (1
jcv). The topology cartoon displayed by software available on the WWW site. In
the cartoon, triangles represent beta strands and circles helices. The direction
of the strands is implied by the orientation of the triangles: "up" (out of the
plane of the page) strands are drawn as up triangles and "down" strands as down
triangles. The peptide chain runs from N1 to C2. The structure of the fold as a
sandwich made of two anti-parallel beta sheets is clear from the cartoon.
The atlas of topology cartoons was generated from the version of the PDB current
on July 1, 1997. In order to avoid the generation of many duplicate cartoons,
the chains present in the database were first clustered at a sequence similarity
threshold of 95%. Chains consisting of nucleic acid sequences were removed, as
were protein chains of less than 30 residues. From an original total of 10534
chains this produced 2144 clusters of near-identical sequences. From each
cluster a representative TOPS diagram was produced from a single structure. This
was chosen to be the highest resolution X-ray structure in the cluster, or an
NMR structure if no X-ray structures were available. Within a chain, each
structural domain was plotted separately using domain definitions taken from the
CATH1 protein structure classification.
The cartoons were generated automatically, in the first instance, using a
substantially modified version of the program TOPS 2. While the original version
of TOPS would produce satisfactory cartoons for simpler protein folds, it was
found to be unable to do so for many more complicated folds. The modifications
were necessary in order to increase the success rate of the program sufficiently
to make automatic generation of a large number of cartoons a viable proposition.
The generation of the atlas of cartoons was viewed as a test of the new version
of the program. Each cartoon in the atlas was checked manually with the 3D
structure of the protein, and the success rate in producing satisfactory
cartoons was found to be 82%. Among the failures were many cartoons which were
correct but not aesthetically pleasing, but there were still some complicated
folds for which the program failed. The cartoons judged to be failures were
corrected by hand editing and included in the atlas.
The atlas is viewed using an applet (a program written in the Java programming
language, delivered over the WWW, and run on the client machine). A basic applet
using Java version 1.0 simply allows the user to view the cartoons, while users
with a WWW browser supporting Java version 1.1 can use a much more functional
applet which allows editing and printing of the cartoons. The same applets are
used for viewing, editing, and printing cartoons generated at the request of the
user by the server facility. Some users with older machines and/or browsers have
experienced difficulties with the Java technology and for this reason a purely
HTML/GIF version of the atlas will be provided in the near future
We hope to keep the atlas up to date as new structures arrive in the PDB.
However, because updates to the atlas require significant effort, we anticipate
that there will always be a time lag between structures arriving in the PDB and
cartoons being put into the atlas. In this case users will be able to use the
server to generate their own cartoons for the new structures. The software used
in the generation of the atlas will be made available in some form, and details
will be posted on the Web site.
Acknowledgements
We are grateful to Dr. T. P. Flores for giving us the source code for TOPS and
allowing us to modify it without restriction. We are also grateful to Dr. C. A.
Orengo for providing us with the domain boundary file associated with the CATH1
protein structural domain classification.
References
Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. &
Thornton, J. M. (1997). CATH--a hierarchic classification of protein domain
structures. Structure, 5, 1093-1108.
Flores, T. P., Moss, D. S., & Thornton, J. M. (1994). An algorithm for
automatically generating protein topology cartoons. Prot. Eng. 7, 31-37.
--------------------------------------------------------------------------
SARF2 - a Program for Comparison of Protein Structures
Nickolai N. Alexandrov
Amgen, Thousand Oaks, CA, USA (nicka@amgen.com,
http://www-lmmb.ncifcrf.gov/~nicka/info.html)
Discovering new similarities in protein structures is an extremely exciting
process. It is especially interesting if proteins are not sequentially related
and so the structural similarity is completely unexpected. Obviously, when you
find a structural resemblance, you have two problems: first, you need to prove
that the similarity is significant, and, second, you need to explain the
biological meaning of this similarity. Traditionally the significance of the
match is demonstrated by an unusually large number of C-alpha atoms which can be
superimposed with a small root mean square distance (rmsd). Biological meaning
can be explained by the evolutionary relationship of the proteins, similar
functional properties, and/or energetic stability of the 3D motif.
There are several programs for protein structure comparison recently reviewed by
Gibrat et al. (1996). However, finding common motifs in 3D structures is not a
trivial problem. Probably the most difficult part here is to think up a measure
of similarity between two structures which correlates with biological sense.
Usually a similarity between two structures is described in terms of the number
of C-alpha atoms and the rmsd between them. Yet, these numbers do not provide an
adequate measure of structural similarity. For example, isolated residues with a
small rmsd are likely to form a less significant match than a spatial
arrangement of continuous backbone fragments.
The program SARF2 (Alexandrov, 1996) detects common motifs in protein structures
which consist of similarly-arranged backbone fragments. (The abbreviation SARF
stands for Spatial ARrangement of backbone Fragments and was first used by
Alexandrov et al., 1992.) There are two kinds of the spatial resemblance:
topological and non-topological similarities. Topological equivalence assumes
that the fragments in both proteins are connected in the same sequential order.
Non-topological similarities are relatively rare. An example of the non-
topological structural similarity is four-helical bundle motif, in which helices
can be differently connected, but still remain within the same protein
architecture. SARF2 is able to detect both kinds of similarities.
The Web site for SARF2 in the Laboratory of Experimental and Computational
Biology at the National Cancer Institute (http://www-
lmmb.ncifcrf.gov/~nicka/info.html) allows you to compare just two structures. If
you want to compare many protein structures, you can download the program from
the ftp site (ftp://ftp.ncifcrf.gov/pub/SARF2/) and run it on your SGI or DEC
Alpha machine. There are mirror Web sites for SARF2 at the Baylor College of
Medicine (http://defrag.bcm.tmc.edu:9503/lpt.html), at the GMD/SCAI in Germany
(http://cartan.gmd.de/nick/run2.html), and at the Sanger Centre in England
(http://genomic.sanger.ac.uk/).
An important and still open question in protein structure comparison is an
evaluation of the significance of the match. One way to solve this problem is to
compare the structure of interest with all of the PDB and plot the distribution
of the number of matched residues for each structure. The significance of the
match can then be measured in the units of standard deviation from the mean of
this distribution. This approach has been used by Alexandrov and Fischer (1996)
to make a classification of the representative list of protein structures.
A knowledge of the mechanism of protein function is sometimes a useful argument
for the significance of the match. Frequently, active sites are surrounded by a
similar structural environment, although the protein function can be different.
And, vice versa, detection of an unexpected statistically significant structural
similarity can lead to new speculations on the mechanism of protein function.
The most interesting structural similarities are those between proteins with low
amino acid identities. Understanding the origin of these similarities provides a
deeper insight into the mystery of protein folding. The fact that the number of
structural classes is smaller than the number of different sequence families
encouraged many researchers to apply a variety of sequence-structure
compatibility (threading) methods. One of these methods (program 123D), based on
the contact capacity potentials, is also presented on the same NCI web site:
http://www-lmmb.ncifcrf.gov/~nicka/info.html.
References:
Alexandrov, N. N. (1996). SARFing the PDB. Protein Eng. 9, 727-732.
Alexandrov, N. N., Fischer, D. (1996). Analysis of topological and
nontopological structural similarities in the PDB: new examples with old
structures. Proteins, 25, 354-365.
Alexandrov, N. N., Takahashi, K., & Go, N. (1992). Common spatial arrangements
of backbone fragments in homologous and non-homologous proteins. J. Mol. Biol.
225, 5-9.
Gibrat, J. F., Madej, T., & Bryant, S. H. (1996). Surprising similarities in
structure comparison. Curr. Opinion in Struct. Biol. 6, 377-385.
--------------------------------------------------------------------------
Molecular Docking by Fourier Correlation with FTDOCK
Henry A. Gabb and Michael J.E. Sternberg
Biomolecular Modelling Laboratory, Imperial Cancer Reseach Fund, London, UK
(gabb@ibm.wes.hpc.mil, m.sternberg@icrf.icnet.uk)
The ability to predict the binding geometries of biomolecular complexes is
becoming increasingly important with the growing number of individual structures
deposited in the Protein Data Bank because experimental determination of the
structure of biomolecular complexes remains a difficult problem. FTDOCK was
developed to address the problem of docking unbound molecules when the structure
of the complex is unavailable (i.e., predictive docking). FTDOCK implements the
geometric surface recognition algorithm of Katchalski-Katzir and coworkers
(Katchalski-Katzir et al., 1992) to dock two macromolecules. The method takes
advantage of the fast Fourier transform (FFT) to rapidly search the
translational space of two rigidly rotated molecules. An electrostatic function
amenable to the Fourier correlation algorithm has been developed in this
laboratory that improves the final rank of correctly docked molecules (Gabb et
al., 1997). Possible docking orientations are scored for surface complementarity
and favourable electrostatics using Fourier correlation theory. For docking
starting with unbound coordinates, we have shown that in some systems inclusion
of electrostatics is critical to success.
We have used FTDOCK in our laboratory to dock several protein systems for which
the coordinates of the complex and the individual subunits are available (Gabb
et al., 1997). The test set was comprised of six enzyme-inhibitor and four
antibody-antigen complexes. In all but one of our test cases, correctly docked
geometries (interface C-alpha root-mean-square deviation less than or equal to
2.5 Angstroms squared) are found during a complete search of binding space in a
list that was always less than 250 complexes and often less than 30. At this
point, biochemical information is still necessary to remove incorrect
predictions. We found that knowledge of at least one binding site further
improved rankings for correct solutions. For six out of nine test cases, a
correctly docked complex was placed in the top five predictions. For the other
three test cases, two had a correctly docked complex in the top fifteen
predictions and the other had a correct answer in the top fifty. Considering
that 1010 geometries are screened during the global search of binding space,
these results are encouraging. When information about the binding site on both
molecules is available, a correctly docked complex scored in the top five for
eight out of nine test cases. Many of these had the correct answer ranked first
in the list of predictions. Even the worst test case had a correctly docked
complex ranked 27th.
FTDOCK was developed under Irix 5.3 and 6.2, but the program should run on any
UNIX computer. The current version of FTDOCK uses either the fast Fourier
transform from Numerical Recipes Software (Press et al., 1986) or the Silicon
Graphics CHALLENGEcomplib(TM) (Silicon Graphics Inc.) to take advantage of the SGI
shared memory multiprocessor. However, the latter FFT will also run efficiently
on SGI serial computers. A typical docking experiment takes about six hours of
CPU time using eight processors in parallel on a SGI Power Challenge. This
assumes a rotational increment of 15 (6385 nondegenerate rotations). A typical
docking attempt takes 3-4 days on a SGI Indy using the Numerical Recipes FFT
rather than the SGI library routine. In some cases, however, a larger increment
can be used for the rotational search (Katchalski-Katzir et al., 1992). Using an
angular deviation of 20 (2629 nondegenerate rotations), for example, reduces the
computational time to less than one day on a SGI Indy workstation.
FTDOCK can also be used to dock non-protein systems like nucleic acids or small
molecules. Our experiments with non-protein systems have not yet been published.
The program can be obtained via our WWW site
(http://www.icnet.uk/bmm/software.html).
References
Gabb, H. A., Jackson, R. M. & Sternberg, M. J. E. (1997). Modelling protein
docking using shape complementarity, electrostatics, and biochemical
information. J. Mol. Biol., 272, 106-120.
Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Freisen, A. A., Aflalo, C. &
Vakser, I. A. (1992). Molecular surface recognition: determination of geometric
fit between proteins and their ligands by correlation techniques. Proc. Natl.
Acad. Sci. USA 89, 2195-2199.
Press, W. H., Teukolsky, S. A., Vetterling, W. T. & Flannery, B. P. (1986).
Numerical Recipes in Fortran, Cambridge University Press. Available from
Numerical Recipes Software (http://cfata2.harvard.edu/nr/).
Silicon Graphics Inc. (1995) CHALLENGEcomplib(TM) Science and Math Library.
(http://www.sgi.com/Products/Challengecomplib.html).
--------------------------------------------------------------------------
MolView and MolView Lite
Thomas J. Smith
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
(tom@bragg.bio.purdue.edu)
MolView is a program to display and analyze atomic structures and MolView Lite
is a simple rendering program using the new QuickDraw3D technology. Both
freeware applications are currently limited to the Macintosh personal computer,
but work is underway to create a version compatible with WIN95.
MolView has a wide variety of options to examine and display atomic structures.
Atomic structures can be read into MolView as several types of text files: PDB,
O plot files, ChemDraw 3D, and MolView files. Mono and stereo images can be
interactively rotated with the mouse, tool palette buttons, or numerical input.
Key aspects of the structures can be highlighted by mixing the available display
modes: CPK, ribbon, ball&stick, line, and surface stippling. Emphasis has been
placed on the user interface so that users unfamiliar with atomic structures can
easily create figures and perform analysis while still being able to customize
the object's attributes. Users can customize atomic labels and choose atoms for
labeling by clicking on the atom or by picking them from a scrolling list. When
creating ribbon diagrams, the secondary structure elements are either
automatically determined from the structure using psi-phi values and hydrogen
bonding patterns, or read from headers of PDB files. The user can color and
toggle elements of the ribbon diagrams using a palette of buttons that display
the current color, identifies the residue number of the element, and the type of
secondary structure in that segment of the protein. The types of analyses that
can be performed include distance measurements, 3D structural alignments,
Ramachandran plots, Edmunson wheels, hydropathy plots, distance diagrams, B-
value figures, hydrogen bonding patterns, and surface plots. More advanced
users can also display crystallographic and non-crystallographically related
molecules and unit cell boundaries.
There are several options when displaying nucleic acids. A ribbon can be drawn
along the phosphoribose backbone and the ring structures can be color coded by
filling the rings with colored planes. For presentation and educational
purposes, there are several types of files that can be read or written by
MolView. When MolView files are updated, colors, some objects, and the new
orientation matrix are saved in the file. Line drawings, MOL objects, can be
written as separate objects with the color information stored in the header.
Using these objects, students can drag and drop files into MolView to view
prepared structural lessons. Three different types of QuickTime movies can be
created to enhance display performance on older machines or when creating multi-
media resources. The various objects and plots can all be written to object-
oriented PICT files for publication quality images. Simple line drawings can be
saved as DXF files for import into other rendering applications. Finally, all
of the various types of molecular objects can be written to QuickDraw3D (3DMF)
files where they can be read and interactively rendered by a growing number of
applications that run under either MacOS or Windows95 operating systems.
MolView Lite is a simple rendering application that reads and interactively
renders the MolView 3DMF output. The image can be written out as a PICT image
or QuickTime movie.
There are also several other resources available at the MolView WWW site
(http://bilbo.bio.purdue.edu/~tom). Files demonstrating crystallographic and
non-crystallographic symmetry are included in the application package. An
interactive tutorial can be downloaded that takes the user through examples of
the major options and explains many of the terms used in the write-up. The
write-up is available in Word (5.1 and 6.0) and HTML formats. Example images
and movies are also available at this site.
--------------------------------------------------------------------------
OLDERADO: Extracting Single Structures, Core Atoms and Domains from a NMR-
derived Ensemble
Lawrence A. Kelley and Michael J. Sutcliffe
Department of Chemistry, Leicester University, Leicester, UK
(L. Kelley@icrf.icnet.uk, sjm@le.ac.uk).
We have recently developed a WWW server, OLDERADO (On-Line Database of Ensemble
Representatives and Domains; http://neon.chem.le.ac.uk/olderado/) (Kelley &
Sutcliffe, 1997), which identifies the "best" single structure in a NMR-derived
ensemble (Sutcliffe, 1993; Kelley et al., 1996), and determines the "core" atoms
across the ensemble and the domain(s) (or rigid body(ies)) to which these belong
(Kelley et al., 1997). The database component of OLDERADO has been integrated
into the "Atlas" page resulting from a PDB 3DB Browser(TM) search for a NMR-derived
ensemble, and in addition, individual representative MODEL structures for a PDB
entry can be downloaded via the European Bioinformatics Institute (EBI)
(http://www2.ebi.ac.uk/msd/nmr_search.shtml).
OLDERADO consists of two components: (i) a database of NMR-derived ensembles
deposited in the PDB, and (ii) the functionality to upload and analyse a user's
own ensemble of structures. Generation of the OLDERADO database, and processing
of uploaded structures, is performed by two analysis tools: NMRCORE (Kelley et
al., 1997) and NMRCLUST (Kelley et al., 1996). NMRCORE automatically defines
the core atoms and the domains in which these lie. This is achieved using a
sorted list of dihedral angle order parameters (Hyberts et al., 1992) to define
the core, followed by the definition of the domain(s) which comprise the core
using automatic clustering of the variances in inter-atom distances. NMRCLUST
automatically clusters ensemble members into conformationally-related sub-
families. All structures are superimposed in a pairwise manner and the
resulting RMS distance between each pair calculated. These distances are used
as a similarity score on which to base the clustering. Average linkage cluster
analysis is used in conjunction with a novel penalty function to determine a
cut-off in the clustering hierarchy automatically.
At the top of the results page, there is a summary which defines the largest
domain and the "most representative" MODEL entry. Under this are two tables -
the first detailing (in order of domain size) the core and domain(s), and the
second (in order of cluster size) the representative structure(s) and cluster
membership. These domains and clusters can be viewed interactively in three-
dimensions via the "View Domains" and "View Clusters" buttons, respectively.
OLDERADO has also been integrated into the PDB 3DB Browser - it is accessed via
the Atlas page if the result of a search is a NMR-derived ensemble. The link
gives direct access to the OLDERADO database entry for this PDB entry; the
information available is described in the preceding paragraph. Additionally,
the OLDERADO methodology enables users to download via the EBI (with the aid of
Kim Henrick in the Macromolecular Structure Group) an individual MODEL (by
default, the "most representative"), rather than the entire ensemble, from an
existing PDB entry. In cases where a user requires only a single MODEL, or a
set of "representative" models, this reduces the bandwith required for download,
reduces the diskspace required on the local machine, and eliminates the need to
split a downloaded file.
References
Hyberts, S. G., Goldberg, M. S., Havel, T. F. & Wagner, G. (1992). The solution
structure of eglin c based on measurements of many NOEs and coupling constants
and its comparison with X-ray structures. Protein Sci. 1, 736-751.
Kelley, L. A. & Sutcliffe, M. J. (1997). OLDERADO: on-line database of ensemble
representatives and domains. On Line Database of Ensemble Representatives And
DOmains. Protein Sci. 6, 2628-2630.
Kelley, L. A., Gardner, S. P. & Sutcliffe, M. J. (1996). An automated approach
for clustering an ensemble of NMR-derived protein structures into
conformationally related subfamilies. Protein Eng. 9, 1063-1065.
Kelley, L. A., Gardner, S. P. & Sutcliffe, M. J. (1997). An automated approach
for clustering an ensemble of NMR-derived protein structures into
conformationally related subfamilies. Protein Eng. 10, 737-741.
Sutcliffe, M. J. (1993). Representing an ensemble of NMR-derived protein
structures by a single structure. Protein Sci. 2, 936-944.
--------------------------------------------------------------------------
Notes of a Protein Crystallographer -
FRODO, the Electronic Hobbit
Cele Abad-Zapatero
Department of Structural Biology, Abbott Laboratories, Abbott Park, IL, USA
(abad@abbott.com)
From early childhood, John Ronald Reuel Tolkien (J.R.R. Tolkien: 1892-1973) was
fascinated with languages. When he was five, his mother - who was fluent in
Latin, French, and German - taught him to read in all three languages plus her
native English. Fatherless since 1896, the family lived in a small rented
cottage in the hamlet of Sarehole by the Cole River, far from the smokestacks
and soot of Birmingham. The quiet meadows and streams and Sarehole were a haven
for Ronald and his younger brother Hilary. There his mother introduced them to
botany and inspired in them a love for plants, trees and the beauty of natural
landscapes. Nonetheless, change again came to his life abruptly. His mother died
in 1904 and the brothers were left under the guardianship of a Catholic priest,
Father Francis Morgan, who had a tremendous influence on his education and his
life. Tolkien graduated from King Edward VI's school in Birmingham and won an
award to attend Oxford University. His interest and passion for languages led
him to study philology, specializing in the literary and linguistic tradition of
the English West Midlands with extensive knowledge of Anglo-Saxon (or Old
English as in Beowulf), Middle English (the language of Chaucer), and Finnish,
Icelandic, Norse and Germanic mythologies and folklore. He was Professor of
Anglo-Saxon at Oxford and a Fellow of Pembroke College from 1925 to 1945,
Professor of English Language and Literature and a Fellow of Merton College from
1945 until his retirement in 1959.
It is impossible to separate Tolkien's academic achievements from his creation
of two muti-faceted, highly imaginative, epic stories which had a tremendous
influence on the youth of the 1960's all over the world and whose effect still
reverberates today. In 1937 he published The Hobbit (Tolkien, 1994), which
received high acclaim as a fascinating children's story in which he introduced
as main characters a `hobbit' named Bilbo Baggins and a magician of sorts named
Gandalf. Tolkien later wrote that the origin of the word hobbit seems to be: "a
worn-down form of a word preserved more fully in the language of Rohan: holbyta
or `hole-builder'" (Tolkien, 1993b). What is a hobbit? In his own words:
" [..] They are (or were) a little people, about half our height, and smaller
than the bearded dwarves. Hobbits have no beards. There is little or no magic
about them, except the ordinary everyday sort which helps them to disappear
quietly and quickly when large stupid folk like you and me come blundering
along, making a noise like elephants which they can hear a mile off. They are
inclined to be fat in the stomach; they dress in bright colours (chiefly green
and yellow); wear no shoes, because their feet grow natural leathery soles and
thick warm brown hair like the stuff on their heads (which is curly); have long
clever brown fingers, good-natured faces, and laugh deep fruity laughs
(especially after dinner, which they have twice a day when they can get it. Now
you know enough to go on with." (Tolkien, 1994, p.3)
The illusion of hobbits as calm, simple people capable of heroic feats caught on
quickly and Tolkien was asked to write more adventures of Bilbo Baggins. The
Hobbit had ended with Bilbo keeping a ring that he had found during his
encounter with Gollum, and living happily in the Shire: the idyllic part of
Middle-earth where the hobbits lived and that scholars have related to the
Sarehole of Tolkien's childhood (Neimark, 1996). The author had no desire to
write a sequel. Instead, The Fellowship of the Ring, the first volume of the
epic trilogy The Lord of the Rings was published in 1954. Soon after, the next
two volumes appeared: The Two Towers and The Return of the King. The completed
work was a mythological world of monumental proportions in which Tolkien had
given life to creatures, kingdoms, wars, calendars, climates, places,
landscapes, and seasons to give flesh and blood to the languages spoken by the
people of Middle-earth: humans, elves, trolls, goblins, giants, dragons, ents,
balrogs, orcs. The hero was Frodo, heir and nephew of Bilbo Baggins, who
together with his friend Sam and other companions of the fellowship undertake a
quest to destroy the master evil ring of Sauron that Frodo had inherited from
his uncle. The appeal of an innocent, gentle creature succeeding in destroying
the forces of evil against all odds, in an unspoiled landscape of pristine
forests, mountains and lakes was enormous. By 1967, The Lord of the Rings had
been translated into nine languages with an estimated readership of fifty
million people. The graffito: FRODO lives! (Tolkien, 1993a), appeared in the New
York subway as testimony to a cultural phenomenon that had opened a magic
wonderland of places, characters and events unhindered by the prosaic incidents
of our everyday lives. Tolkien had transcended the arcana of scholarly research
in obscure languages to create a universal allegory of the constant struggle of
good against evil, with strong environmental overtones.
FRODO, the electronic hobbit, had its origins in 1976. Whether the younger
generations believe or not, at that time all protein models were built starting
from a C? tracing obtained from markings on an electron density map drawn on
small plexiglass sheets stacked up as "mini-maps" (Jones, 1985). From these
guide coordinates, detailed atomic models were built at a much larger scale on a
Richards optical comparator known in the trade as "Richards Box" or "Fred's
Folly" using Kendrew model parts (Richards, 1985). Glass or plastic windows had
to be drawn by hand with tracings of the electron density contours at the
appropriate scale (2 cm=1 A). Atomic coordinates were laboriously extracted from
this wire model by tedious and often inaccurate protocols (Salemme, 1985). There
was an immediate need for a computerized method that would allow the fitting of
an atomic model to the experimental electron density map, and which would remove
the tedium and inaccuracies from macromolecular structure determination and
refinement (Editorial, 1997).
The idea was floating in the community and several laboratories had initiated
projects to achieve that goal. Drs. J. Gassman and R. Huber found a bright
young Welsh would-be crystallographer who was interested in living in Munich to
develop such a tool, and encouraged him to make it a program useful for the
routine operation in a protein crystallography laboratory. Tradition has it that
the original program sent data back and forth between a PDP11 and a SIEMENS4004,
in a computing environment where many of the programs were named after different
hobbits. It was only natural that the central program will be named after the
most famous of all the hobbits in Tolkien's trilogy. For obvious reasons, the
test version used most of the computing cycles and was called initially SAURON.
FRODO made his appearance in the protein crystallography community twenty years
ago in 1978 (Jones, 1978). As for myself, I got to know FRODO very well in 1981
during three beautiful weeks of immersion during the incomparable Swedish
spring. Our friendship developed during many nocturnal model-building sessions
at the old Wallenberg Laboratory next to the ancient city castle in Uppsala. I
must confess that we had our crises, but he was certainly a very friendly
hobbit. I was the one to blame for every crisis. Quite often, I failed to
understand his prompts or suggestions, and many times his cues made no sense to
me. He was always patient, effective and obedient.
You could CHAT (actual FRODO commands in capital letters) with him via a
keyboard but the most effective way to communicate was with a tablet and a pen
which would allow you to pick and identify atoms, and select different commands
from a MENU on the screen. Obedient to the GO command, FRODO would display for
you a certain volume of electron density and using well designed commands you
could tell him to BREAK certain bonds and cut the protein chain into pieces.
These pieces could then be moved with six degrees of freedom (FBRT) to make them
fit into the three-dimensional electron density maps which could be rotated at
will with dials.
FRODO did not know any protein chemistry, or if he did, he would not explicitly
tell you so. It was you who would organize those constellations of points in
space into a meaningful protein chain by using the REFInement command. He would
faithfully apply the rules of chemistry to certain ZONEs of your spatial points
which were covered by your electron density contours. This was a tremendous help
when trying to fit those old electron density maps. FRODO was also very handy
at modeling exercises by allowing you to create MOLecular objects that you could
use either as background while fitting electron density or as objects of study
in their own right.
For some time, the rumor (joke) floated in the community that the only
documentation for FRODO was "The Lord of the Rings". This might have been true,
but in his own humble way FRODO proved to be a very useful hobbit and was the
ancestor of many other electronic hobbits that are now well settled in our
computer underworld. In addition, his faithful friend SAM was always available
to insert or delete residues, create a sequence and do all the necessary
bookkeeping so that in the end everything was SAVEd in the disk with `amazing
speed' and accuracy. During my visit, FRODO lived in an independent VAX750
computer and his commands were translated into a Vector General VG3400. Later he
lived inside many other boxes or hobbit-holes in many other countries. His
performance improved as his electronic eyes and hands improved, permitting us to
view unimaginable shapes and forms and to examine atomic continents, islands and
landscapes of undescribable complexity and beauty. Following his original
insights, we can now see atomic crevasses and caves, canyons, rivers, mountain
ridges and valleys in different and vivid colours, and subtle hues and shades.
FRODO opened for us an atomic underworld that was beyond our reach before. He
introduced us to an atomic Middle-world that we could not have imagined without
his assistance and that we are just beginning to explore, appreciate and
understand.
One could argue that there are no malicious villains in our atomic Middle-world:
no Dark Riders or Ringwraiths trying to prevent FRODO from destroying the evil
ring. Yet, we routinely encounter, examine, and study molecules with pathogenic
and curative properties in our crystals, and a major part of our time is spent
trying to understand their interactions with themselves and with others. We are
trying to defeat the evil forces of disease, pain and deformity and our
operational domain is the atomic Middle-world that FRODO unveiled for us. There
are parts of these atomic creatures that we cannot see or cannot fit well in our
electron density maps, and that chase us in our sleep like the Dark Riders
chased after FRODO and his friends. However, our true Gollum, Shelob and Sauron
are uncertainty, lack of knowledge, and especially bias and disorder. Those
restrictive forces will always be with us. In the meantime, FRODO will live on
in the heart of those of us who -once upon a time- built protein models using
mechanical parts and read the coordinates of our structures using a two-
dimensional grid and a plumb line. He did so many things for us; he was such
good a friend....
References
Editorial (1997), String and sealing wax. Nature Struct. Biol. 4, 961-964.
Jones, T. A. (1978). A graphics model building and refinement system for
macromolecules. J. Appl. Cryst. 11, 268-272.
Jones, T. A. (1985). Diffraction methods for biological macromolecules.
Interactive computer graphics: FRODO. Methods Enzymol. 115, 157-171.
Neimark, A. E. (1996). Myth Maker: J. R. R. Tolkien, pp. 85-86, Harcourt Brace &
Co., New York.
Richards, F. M. (1985). Optical matching of physical models and electron density
maps: early developments. Methods Enzymol. 115, 145-154.
Salemme, F. R. (1985). Some minor refinements on the Richards optical comparator
and methods for model coordinate measurement. Methods Enzymol. 115, 154-157.
Tolkien, J. R. R. (1993a). The Lord of the Rings Trilogy. Part One: The
Fellowship of the Ring.Intro by Petr Bearle, Authorized edition of the fantasy
classic by Ballantine Books, New York.
Tolkien, J. R. R. (1993b). The Lord of the Rings Trilogy. Part Three: The Return
of the King. Appendix F. Authorized edition of the fantasy classic by
Ballantine Books, New York.
Tolkien, J. R. R. (1994). The Hobbitt. 2nd Ed. Houghton Mifflin Company, New
York.
--------------------------------------------------------------------------
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VMD - Visual Molecular Dynamics
http://www.ks.uiuc.edu/Research/vmd/
X-PLOR Home Page
http://xplor.csb.yale.edu/
Other Resources
Crystallography Worldwide
http://www.unige.ch/crystal/w3vlc/crystal.index.html
BioMoo
http://www.cco.caltech.edu/~mercer/htmls/BioMOOHomePage.html
DALI - Comparison of Protein Structures in 3D
http://www.embl-heidelberg.de/dali/dali.html
NCSA Biology Workbench
http://biology.ncsa.uiuc.edu/
MOOSE (Macromolecular Structure Database
at San Diego Supercomputer Center)
http://db2.sdsc.edu/moose
PDB_select: Representative PDBStructures
ftp://ftp.embl-
heidelberg.de/pub/databases/protein_extras/pdb_select/recent.pdb_select
PROCHECK - To Submit a PDB File for Analysis
http://www.cryst.bbk.ac.uk/PPS/procheck/test.html
Protein Structure Verification-Biotech Server
http://biotech.embl-heidelberg.de:8400/
Mirrored at Protein Data Bank
http://biotech.pdb.bnl.gov:8400/
Resources for Macromolecular Structure Information
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Weizmann Institute, Genome and Bioinformatics
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Protein Data Bank
Biology Department, Bldg. 463
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000 USA
Telephone +1-516-344-3629
Fax +1-516-344-5751
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Number of Entries Deposited (Bar)
and Average Time to Release (Line)
Accumulated and Averaged on a Quarterly Basis
[image not available as text]
Bar Graph - Number of Entries in the Following Categories:
OnHold - (light blue) On-hold per depositor request
Processing - (white) Being processed
Released - (black) Released
Line Graph - Average Number of Days to Release
The data were accumulated and averaged on a quarterly basis. The average turn-
around times for entries now being processed are estimated based on the average
of the last 12 months.
Data for the last quarter are accumulated until the date specified on the graph.
See http://www.pdb.bnl.gov/pdb-docs/EntryTurnAround.html for regularly updated
plot.
--------------------------------------------------------------------------------
Protein Data Bank
Biology Department, Bldg. 463
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000 USA
Telephone +1-516-344-3629
Fax +1-516-344-5751