The Protein Data Bank:Current Status and Future Challenges

Joel L. Sussman1,2, Enrique E. Abola1, Nancy O. Manning1 and Jaime Prilusky1,31Protein Data Bank, Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000, USA

2Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel3Bioinformatics Unit, Weizmann Institute of Science, Rehovot 76100, Israel

jls@bnl.gov; http://www.weizmann.ac.il/~jsgrp/joel.htmlabola1@bnl.govoeder@bnl.gov

lsprilus@weizmann.weizmann.ac.il; http://bioinformatics.weizmann.ac.il/jaime_prilusky.html

Abstract

The Protein Data Bank (PDB) is an archive ofexperimentally determined, three-dimensional structuresof proteins, nucleic acids, and other biologicalmacromolecules. The PDB is now being transformed into3DB, the Three-Dimensional Database ofBiomacromolecular Structures, with significantlyenhanced capabilities.

1 Introduction

The Protein Data Bank (PDB) is an archive ofexperimentally determined, three-dimensional structures ofproteins, nucleic acids, and other biologicalmacromolecules [1, 2]. PDB has a 25-year history ofservice to a global community of researchers, educators,and students in a variety of scientific disciplines [3]. Thecommon interest shared by this community is a need toaccess information that can relate the biological functionsof macromolecules to their three-dimensional structures.The PDB is now being transformed into 3DB, the Three-Dimensional Database of Biomacromolecular Structures,which will continue to operate from Brookhaven NationalLaboratory.

The challenge facing the new 3DB is to keepabreast of the increasing flow of data, to maintain thearchive as error-free as possible, and to organize andpresent the stored information in ways that facilitate dataretrieval, knowledge exploration, and hypothesis testing,without interrupting current services. The PDB hasintroduced substantial enhancements to both datamanagement and archive access in the past two years, andis well on the way to converting to a more powerfulsystem that combines the advantages of object-orientedand relational database systems. 3DB will transform PDBfrom a Data Bank serving solely as a data repository intoa highly sophisticated knowledge-based system forarchiving and accessing structural information. Theprocess will be evolutionary, insulating users from drasticchanges, and will provide both a high degree ofcompatibility with existing software and a consistent userinterface for casual browsers.

Development is underway for 3DB to operate asa direct-deposition archive, providing mechanisms fordepositors to submit data over the Internet with minimalstaff intervention. Data archived in 3DB is managed usingthe Relational Database Management System (RDBMS),SYBASE [4]. The new database (3DBase) is beingdeveloped with a view to being a member of a federationof biological databases. Collaborative international centersare also being established to assist in data deposition,archiving, and distribution activities.

2 Resource Status, September 1996

Rapid developments in preparation of crystals ofmacromolecules and in experimental techniques forstructure analysis and refinement have led to a revolutionin Structural Biology. These factors have contributedsignificantly to an enormous increase in the number oflaboratories performing structural studies ofmacromolecules to atomic resolution and the number ofsuch studies per lab. Advances include: 1) recombinantDNA techniques that permit almost any protein or nucleicacid to be produced in large amounts; 2) better X-raydetectors; 3) real-time interactive computer graphicssystems, together with more automated methods forstructure determination and refinement; 4) synchrotronradiation, allowing the use of extremely tiny crystals,Multiple Wavelength Anomalous Dispersion (MAD)phasing, and time-resolved studies via Laue techniques; 5)NMR methods permitting structure determination ofmacromolecules in solution; and 6) electron microscopy(EM) techniques, for obtaining high-resolution structures.

These dramatic advances produced an abrupttransition from the linear growth of 15-25 new structuresdeposited per year in the PDB before 1987 to a rapidexponential growth reaching the current rate of ~25deposits per week (Fig. 1).

This rapid increase overwhelmed PDB staffresources and data processing procedures and, by mid-1993, a backlog of some 800 coordinate entries hadaccumulated. This backlog was eliminated by January1994 by increasing automation of processing and hiringadditional staff. In all, more than 4,250 of the ~5,350

current PDB coordinate entries (~80%) have beenprocessed since 1991.

0

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73 75 77 79 81 83 85 87 89 91 93 95

NMRX-ray

Figure 1 PDB Coordinate Entries Available

Table 1 is a summary of the contents of PDB.Present plans are to keep abreast of the deposition ratewith a timeline of three months from receipt to finalarchiving, which includes the time that the entry is withthe depositor for checking. This timeline is comparable tothe publication schedules of the fastest scientific journals.

PDB Archive Contents5346 released atomic coordinate entries576 structure factor files243 NMR restraint files

Molecule type4748 proteins, peptides, and viruses213 protein/nucleic acid complexes373 nucleic acids12 carbohydrates

Experimental Technique4441 diffraction and other758 NMR147 theoretical modeling

Table 1 PDB Archive Contents - Jan 1997

In the same period, the proliferation andincreasing power of computers, the introduction ofrelatively inexpensive interactive graphics, and the growthof computer networks greatly increased the demand foraccess to PDB data (Fig. 2). The requirements ofmolecular biologists, drug designers, and others inacademia and industry are often fundamentally differentfrom those of crystallographers and computationalchemists, who have been the major users of the PDBsince the 1970s.

PDB entries are available on CD-ROM, whichPC users can search using the PDB-SHELL [5] browser,built using FoxPro [6]. In addition to its browsing

mechanisms, PDB-SHELL provided direct access to themolecular viewing program RasMol [7]. They are alsoaccessible on the Internet via a World Wide Web (WWW)browser, PDBBrowse [8], and an enhanced 3DB Browseras illustrated in Appendix C below, at Brookhaven(http://www.pdb.bnl.gov/) and several mirror sitesworldwide.

0

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Figure 2 FTP data access

The PDBBrowse incorporates a number offeatures that make it easy to access information found inPDB entries. Multiple search strings covering variousfields, corresponding to PDB record types such ascompound, header, author, biological source, or heterogendata, are supported. These searches support boolean 'and','or', and 'not' operators. Entries selected can be retrievedautomatically, and the molecular structures can bedisplayed using the public-domain X-based molecularviewer RasMol (or similar viewer). They also includehypertext links to SWISS-PROT [10], BMRB [11], theEnzyme Commission Database, and the Entrez ReferenceDatabase [13]. Internet access to the archives has becomethe primary mode of retrieving entries from the PDB.However, we continue to receive a considerable number oforders for our CD- ROM product. We anticipate that thiswill continue to be true for a variety of reasons. Forexample, network performance still remains poor in anumber of locations and these disks, released quarterly,provide local access to the contents of the archive. Someof these network access difficulties are easily overcome byinstalling a copy of the PDB FTP and WWW serversusing mirroring software. With this software all files inthe PDB are stored locally and any changes areautomatically reflected on a daily basis.

3 The 3-Dimensional Database ofBiomacromolecular Structures (3DB)

Implementation of the conversion of PDB to 3DB isentailing changes in every aspect of current operations. Anew data submission and archival system is beingimplemented, which attempts to balance the need for fullautomation with the need to maintain very high levels of

data accuracy and reliability. The new system relies on anRDBMS for data management and archival. An overviewof the relationships between 3DBase and depositors,users, third-party software developers, and other databasesis shown in Fig. 3. The following sections provide asummary of development work.

ValidationAnnotation

depositor

Query Analyzer

OutputGenerator

user 3rd party

GDB

PMD

CitDB

SWISSENZYME

BMRB

PIRCSDB

NDB

GenBankNCBI

3DBase

NDBEBIBMRB

Figure 3 3DBase relationships.

3.1 The 3DBase - A Relational DatabaseManagement System for 3DB

The 3DBase is constructed with the SYBASE RDBMS,the Object-Protocol Model (OPM), and the OPM datamanagement tools [14] developed by Victor Markowitz'sgroup at Lawrence Berkeley National Laboratory.SYBASE provides a powerful and robust environment fordata management, the OPM tools allow rapiddevelopment of SYBASE databases, and OPM's object-oriented view provides a scientifically intuitiverepresentation of data. Along with a graphical schemaeditor, Markowitz's group distributes a number of otherdevelopment tools. Foremost of these is a schematranslator that generates SQL statements for buildingtables, indices, constraint rules, and triggers.

This development effort attempts to address theneeds of the diverse user community served by the PDB.

The schema supports queries by those interested inanswers to both crystallographic and molecular biologyquestions. The system is being designed with theexpectation that it will shortly be federated with otherbiological databases. Our hope is that federation willpermit complex queries to be submitted to our database,returning a composite answer built from a set of diversedatabases. Interoperability is addressed through the use ofschema sharing with other OPM-based databases andsupport for a variety of data interchange formats in thequery results. In addition to providing users with apowerful environment to do complex ad-hoc queries,3DBase will also facilitate management of the growingarchive, which is expected to contain over 30,000structural reports by the year 2000.

This work is being done as a collaborationamong the following groups:

• The Protein Data Bank - Brookhaven NationalLaboratory

• Bioinformatics Unit - Weizmann Institute ofScience

• OPM Data Management Tools Project - LawrenceBerkeley National Laboratory

• The Genome Data Base - Johns Hopkins University

3.2 Schema Development

OPM is a semantic data model that includes constructsthat are powerful enough to represent the diversity andcomplexity of data found in PDB entries. OPM hasconstructs such as object class, object attribute, classhierarchy and inheritance, and derived attribute. A schemafor 3DBase has been developed using OPM and isavailable for perusal through the PDB WWW home page.Among its notable features is a description of thecoordinate data set from two perspectives. The object classoExperiment provides users with the classical view of aPDB entry which is a report of crystallographic or NMRanalysis. An alternative view is presented in the classoMacroMolecule that describes the biologically activeform of the molecule. Appendix A provides a descriptionof these object classes. A clear example that demonstratesthe differences between these classes is the case of thehemoglobin molecule. The oExperiment object containsthe coordinates for the crystallographic asymmetric unit,which is usually a dimer. The full tetramer will, however,be presented in the oMacroMolecule object. The latter caseis normally what molecular biologists are interested inwhen accessing PDB entries. However, crystallographerswishing to do packing studies or further refinement willneed access to the oExperiment object.

In 3DBase, literature citation data are beingloaded into the CitDB database of references that wasdeveloped by GDB [15]. A pointer to the appropriateentry in CitDB is loaded in the oExperiment object of3DBase. This is an example of the strategy that we arefollowing in linking to external databases. CitDB will be

managed as a federation run by a number of databasecenters that include GDB and PDB. There are severaladvantages to this scenario. By sharing the schema andmanagement of the citation databases, access toinformation stored in each of the databases via thebibliographic citation becomes straightforward.Duplication of effort is also minimized. Today, it is stillcommon to have several public databases build andmaintain their own bibliographic databases. This will nolonger be economically feasible with the expected rapidgrowth in database size.

3.3 Building Semantic Links to ExternalData Sources

Links to contents of sequence databases are provided in3DBase via the oPrimarySeq and oSeqAdv classes. Theseclasses form another set of objects that link 3DBaseobjects to external databases. Representing, building, andmaintaining these links will be one of 3DB's primarytasks in the coming years. There are several issues thatmust be addressed for this effort to succeed. Datarepresentation issues are foremost. Each database usesdifferent data models to represent and store information.Semantic contents are rarely the same; for example, theprimary sequence data stored in sequence databases suchas SWISS-PROT or PIR [16, 17] are presented using aview which differs significantly from that used by PDB.

In general, PIR and SWISS-PROT entriescontain information on the naturally occurring wild-typemolecules. Each entry normally contains the sequence ofone gene product and some entries include the completeprecursor sequence. Annotation is provided to describeresidue modifications. In both databases, the residuenames used are limited to the 20 standard amino acids.

In contrast, PDB entries contain multichainmolecules with sequences that may be wild type, variant,or synthetic. Sequences may also have been modifiedthrough protein engineering experiments. A number ofPDB entries report structures of domains cleaved fromlarger molecules.

The oPrimarySeq object class was designed toaccount for these differences by providing explicitcorrelations between contiguous segments of sequences asgiven in PDB ATOM records and PIR or SWISS-PROTentries. Several cases are easily represented using thisclass. Molecules containing heteropolymers will be linkedto different sequence database entries. In some cases, suchas those PDB entries containing immunoglobulin Fabfragments, each PDB chain may be linked to severaldifferent SWISS-PROT entries.

This facility is needed, because these databasesrepresent sequences for the various immunoglobulindomains as separate entries. oPrimarySeq should also beable to represent molecules engineered by altering the gene(fusing genes, altering sequences, creating chimeras, orcircularly permuting sequences). In addition, it will be

possible to link segments of the structure to entries inmotif databases (e.g., PROSITE [18], BLOCKS [19]).

Initial building of these links is straightforwardand requires analysis of a few entries coming out of aFASTA [20] or BLAST [21] search against the sequencedatabases. What may be problematic in the long run willbe updating these links as new experimental evidence isencountered, leading to a correction in either database.Both PIR and SWISS-PROT have similar problems asthey build pointers to PDB entries. To help obviate thesedifficulties we have agreed to establish a closer interactionbetween the databases. We are setting up a protocol thatwill broadcast to each database changes that could, inturn, affect specific entries.

4 Data Deposition

3DB will operate as a direct-deposition archive, providingmechanisms that will allow depositors to load data withminimal staff intervention. This strategy is essential if3DB is to meet present projections of exponential growthin depositions against a fixed staff size. This isparticularly challenging due to the complexity of the databeing handled, the need for a common viewpoint of theentry description, and the community requirement thatthese data be accessible immediately upon receipt.

With direct deposition, there will be aconcomitant need to increase the power of data validationprocedures. These procedures must reflect current modelsfor identifying errors and must be as complete as possible.Quality control issues assume a more central and difficultrole in direct deposition strategies. Distributed data mustbe of the highest quality; otherwise, users will lose theirtrust in the archived data and will have to revalidate datareceived from 3DB before using them, clearly anunproductive scenario.

4.1 Current Data Deposition Procedures

Since its inception in 1971, the method followed by thePDB for entering and distributing information hasparalleled the review and edit mode used by scientificjournals. Currently, the author submits information whichis converted into a PDB entry and is run against PDBvalidation programs by a PDB processor. The entry andthe output of the validation suite are then evaluated by aPDB scientific staff member, who completes theannotations and returns the entry to the author forcomment and approval. Table 2 summarizes checksincluded in our current data validation suite. Correctionsfrom the author are incorporated into the entry, which isreanalyzed and validated before being archived andreleased.

Originally data flow was a manual system,designed for a staff of 1-2 scientists, and a deposition rateof about 25-50 entries per year. One person processed anentry from submission through its release. By the late

1980s, when the first steps at automation were beingintroduced, running the validation programs took about 4hours per entry. Today, the same step, which includes avastly improved set of validation programs, takes aboutone minute. Graphical viewing of data, a useful andpowerful annotating and checking tool, has been availableto processors since 1992.

Class What is checkedstereochemistry bond distances & angles,

Ramachandran plot (dihe-dral angles), planarity ofgroups, chirality

bonded/non-bondedinteractions

crystal packing, unspeci-fied inter- and intraresiduelinks

crystallographicinformation

Matthews coefficient, Z-value, cell transformationmatrices

noncrystallographic transformation

validity of noncrystallogra-phic symmetry

primary sequence data discrepancies withsequence databases

secondary structure generated automatically orvisually checked

heterogen groups identification, geometryand nomenclature

miscellaneous checks solvent molecules outsidethe hydration sphere,syntax checks, internal dataconsistency checks

Table 2 Data validation with current system

The current deposition load of ~100 entries amonth is handled by about ten staff members whoannotate and validate entries. The process is a productionline in which checking is repeated at various steps toensure that errors and inconsistencies in datarepresentation are minimized. Prior to June 1994, asignificant number of depositions required thatadministrative staff manually input information providedin a deposition form. Introduction of the currentElectronic Deposition Form, together with a new parsingprogram, has greatly reduced hand entry of information.

Today, most of the processing time is spentresolving data representation issues and ensuring thatoutliers are identified and annotated. The mosttroublesome areas are consistently those involvinghandling of heterogens, resolving crystal packing issues,representing molecules with non-crystallographicsymmetry, and resolving conflicts between the submittedamino acid sequence and that found in the sequencedatabases. Publications and other references are sometimesconsulted to verify factual information such as crystaldata, biological details, reference information, etc.

Processing programs, although much improved over thoseused in 1991, still allow errors to pass undetected throughthe system, requiring a visual check of all entries. Wecontinually improve these programs and also acquiresoftware from collaborators to address deficiencies thatboth we and our users have identified. In addition, wenow have formed a quality control group that will beidentifying sources of errors and recommending steps toimprove data quality.

4.2 Development of Automatic Depositionand Validation

3DB must overcome many challenges for directdeposition to work. In a recent workshop held to assessthe needs of 3DB users, crystallographers and NMRspectroscopists were unanimous in their desire for asystem that did not require additional work on their partwhen depositing data. On the other hand, consumers (whoincluded these same depositors) were vocal in their desirefor entries to contain more information than is currentlyavailable within the PDB. We are striving to develop asuite of deposition and validation programs thataccommodates these somewhat conflicting desires whileensuring that the archives maintain the highest standard ofaccuracy. A schematic of the automatic deposition processis depicted in Fig. 4.

AnnotationValidation

AutoDepVerificationAnnotation

PDB/CIF Files

outliers

3DBase

depositor

Figure 4 3DBase automatic validation.

A considerable variety of information is archivedabout each structure which must be supplied by theauthors. The AutoDep program, currently under

development, is expected to simplify the depositionprocess. It includes a convenient and interactive electronicdeposition protocol that guides the author in providinginformation. It also contains tools for data verification andvalidation, and is able to flags errors in syntax orspelling. The form requests approximately 500 items,including a description of the experiment and themolecule under study. Steps are being taken to help easethe burden of filling out this form. For example, theprogram can fill in fields using data from an existingPDB entry. These data can then be modified to reflect thecontents of the new deposition. Checks against otherdatabases are an important and evolving part of thisprocess. Thus, names of organisms are checked against thetaxonomy database of the National Center forBiotechnology Information (NCBI) [22], chemical namesagainst IUPAC [23] nomenclature tables, and authornames and citations against MEDLINE [24] (CitDB whenit becomes available). FASTA/BLAST programs are runagainst the SWISS-PROT and PIR databases to verifyprotein sequences, and variant and mutant sequences arechecked against the Protein Mutant Database [25] (PMD).Links between the PDB/3DB entry and these databases areestablished in the process. To handle the increasingnumber of entries with nonstandard residues (heterogens),a standard residue and heterogen dictionary is beingdeveloped to be used in the data entry and checkingprocess. We are also adopting programs developed by theCambridge Crystallographic Data Center [26] (CCDC),and elsewhere, to handle heterogens automatically for usein AutoDep.

In addition to the deposition form that is filledout by AutoDep, authors are requested to submit thecoordinate data entry and other experimental data files forprocessing and archiving. Facilities are provided byAutoDep that simplify this process. An FTP script isprovided that uploads author-specified local filenames tothe PDB server site.

The completed form is then convertedautomatically into a file in PDB format and, along withthe coordinate data, is submitted to a set of validationprograms for checking and further annotation. Theseprograms are designed to check 1) the quality,consistency, and completeness of the experimental data; 2)possible violations of physical or stereochemicalconstraints (e.g., no two atoms in the same place,appropriate bond angles, etc.); 3) compliance with ourdata dictionary (syntax checks); and 4) in the near future,the correspondence of the experimental data to the derivedstructure. Development of the validation suite will evolvewith advice from the community and encompass programscurrently in use, written both within and outside PDB.

The validation software automatically generates,and includes in the entry, measures of data quality andconsistency, as well as annotations giving details ofapparent inconsistencies and outliers from normal values.This output is returned to the depositor for review. Entrieswhose data quality and consistency meet appropriate

standards may then be sent by the depositor directly forfinal review by the PDB staff and entry into the database.Entries that do not pass the quality and consistencychecks may be revised by the depositor to correctinadvertent errors; alternatively, more experimental workmay be needed to resolve problems uncovered.

Apparent inconsistencies or outliers may remainin a submitted entry, provided these are explained by thedepositor in an annotation. In the most interesting cases,unusual features are a valid and important part of thestructure. However, all such entries will be reviewed forpossible errors by 3DB staff, who may discuss anyimportant issues with the depositor. 3DB staff will thenforward acceptable entries to the database.

To make automatic deposition as easy aspossible, we are working with developers of softwarecommonly used by our depositors. By modifying theseprograms to produce compliant data files and performingvalidation and consistency checks before submission, itmay be possible to bypass most of the tedious steps indeposition. We are already working with Dr. A. Brüngerto use procedures available through X-PLOR [27] toreplace part of the validation suite for structures producedby X-ray crystallography and NMR. Diagnostic outputwill be included automatically as annotations in the entry.A limited version of X-PLOR will be available from BNLto all depositors for validation purposes only.

Validation of coordinate data againstexperimental X-ray crystallographic data requires access tostructure factor data that are requested by PDB, theInternational Union of Crystallography (IUCr), and somejournals, but are not always supplied by the depositor. Weare working toward building consensus in the communitythat structure factor data are a necessary component ofdeposits of structures derived by X-ray crystallography.Statistics such as number of F's and R-values vs.sin(theta)/lambda, etc. will be calculated and included inthe 3DB entry as annotation for the experiment.

In order to make it easier for depositors tosubmit structure factors (as well as to exchange these databetween laboratories), the PDB, in close collaborationwith a number of macromolecular crystallographers, hasdeveloped a standard interchange format for these data.This standard is in CIF (Crystallographic InformationFile) [28, 29] and was chosen both for simplicity ofdesign and for being clearly self-defining, i.e., the filecontains sufficient information for the file to be read andunderstood by either a program or a person. Details of thisformat are available through the PDB WWW server.

A consensus is still developing in the NMRcommunity as to what types of experimental data shouldbe deposited and what kinds of validation and consistencychecks should be performed. Structural data produced byother methods may also have special features that shouldbe archived or checked, for example the sequencealignment used for modelling studies. Requirements forthe types of data to be deposited and proper ways ofchecking the validity and consistency of the data will be

developed in cooperation with the experimentalcommunity for each category of structure data archived bythe 3DB.

4.3 AutoDep's Most Important Features

• The ability to fill in the form automatically froman existing PDB entry or from a previousdeposition. When the depositor pushes a button,AutoDep will enter data from the designated file tothe appropriate fields in the new form. The authormerely has to update fields to reflect the newstructure.

• X-ray structural refinement software is available towrite PDB records that can be automaticallymerged into the deposition form. For example, thenew releases of X-PLOR [27] and SHELX-96 writerefinement details as PDB records which will beread by the program and entered in the relevantsections. We are continuing to work with authorsof various programs and anticipate that increasingnumbers of programs will be integrated with PDB.

• Each session has help files, examples, and links torelated documentation and useful URLs to supportthe author during the AutoDep session.

• At any time during the AutoDep session, theDeposition Form or the resultant header portion ofthe PDB file can be viewed to check progress.

• The AutoDep session can be interrupted at any timeand resumed hours, days, or even weeks later. Thesession ID number and password must be recordedto continue with the same deposition.

• When an author is satisfied with the completedDeposition Form, a submit button is provided thatinitiates the following:• The coordinates are passed through a syntax

checker.• If they fail, the depositors is asked to correct the

problem and resubmit the coordinates.• If they pass, the depositor is immediately sent an

acknowledgement letter containing the PDB IDcode.

• The entry enters the PDB processing flow.

5. Accessing Data in 3DBase

User queries to 3DBase will be via the network usinggeneral purpose graphical user interfaces such as Mosaicand Netscape. Access will also be possible through theuse of software developed by third parties (commercialdevelopers). As diagrammed in Fig. 5, user queries willbe addressed to the Query Analyzer (3DB-QA), a programmodule running at the server site that will parse queriesand pass them on to 3DBase. Query results will be

returned through the Output Generator (3DB-OG) in theformat requested by the user. Queries placed over thenetwork will generally be in the form of URLs, which areeasily generated from HyperText links, HTML-basedforms, or by use of programs or scripts employing theNational Center for Supercomputing Applications libraries[30] for more sophisticated applications. As part of thequery the user may specify the format of the response, aswe do at the present time in the PDB WWW browser. Theresponse will be frequently in the form of an HTMLdocument, but it can also be a PDB- or CIF-formatted file[28, 29]. The conversion is done using pdb2cif [32]. Theinformation returned may be either a complete or partialentry, and may include information from linked databasesor external programs.

QueryAnalyzer

3DBase

direct DBaccess

user

OutputGenerator

PDB (plain/HyperText)

bcp...

CIF (plain/HyperText)3rd partyusers

WWW client(Netscape, ...)

Figure 5 Accessing 3DBase

A 3DBase browser has been built using StanLetovsky's Genera system. Users specify search criteria byfilling out an HTML form. Software at BNL processesthis form and generates the required SQL. Systemperformance is improved by using stored SYBASE SQLprocedures that access each predefined object. The fieldsavailable are similar to those in our PDBBrowse program,and answer most of the questions that users have beenasking.

For those familiar with (or willing to learnabout) the OPM protocol, access to the object layer willbe provided using a high-level, OPM-based querylanguage. As part of the 3DB open database policy, directaccess to the underlying RDBMS will be allowed andactively supported. These queries are not parsed by the3DB-QA module, so better response time can be expected.This provides third-party developers with the opportunityeither to incorporate SQL clients in their products or tolearn more of the OPM protocol and, thereby, gain accessto all of the benefits that the Object model affords (e.g.,active external links, programs, etc.). As depicted in Fig.5, the output generator will return query results using avariety of data interchange formats. PDB will continue tosupport its current format in the foreseeable future. Wealso plan to extend this format to allow us to representobjects being stored in 3DBase. In addition, a "raw

format" is being provided which returns an attribute/valuepair. This form is easily parsed and is more compact thanthe PDB format.

6. References

[1] F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F.Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T.Shimanouchi, and M. Tasumi, The Protein Data Bank: aComputer-based Archival File for MacromolecularStructures, J. Mol. Biol., Vol. 112, pp. 535-542 (1977).

[2] E. E. Abola, F. C. Bernstein, S. H. Bryant, T. F. Koetzle,and J. Weng, Protein Data Bank, in CrystallographicDatabases - Information Content, Software Systems,Scientific Applications, F. H. Allen, G. Bergerhoff, andR. Sievers, eds., Data Commission of the InternationalUnion of Crystallography, Bonn pp. 107-132 (1987).

[3] Crystallography, Protein Data Bank [announcement],Nature New Biology Vol. 233, pp. 223 (1971).

[4] SYBASE SQL Server (Unix version 10.0) [computerprogram] (1994). Available Distributor: Sybase Inc.,Emeryville, CA USA.

[5] PDB-SHELL [computer program, on-line and CD-ROM].Available anonymous FTP: ftp.pdb.bnl.gov.

[6] Microsoft FoxPro Relational Database ManagementSystem [computer program]. Available Distributor:Microsoft Corporation, Redmond, Washington 98052-6399 USA.

[7] R. Sayle, RasMol [computer program]. Availableanonymous FTP: ftp.dcs.ed.ac.uk. Directory:/pub/rasmol. File: README [for filenames for differentplatforms].

[8] D. R. Stampf, C. E. Felder, and J. L. Sussman,PDBBrowse - a Graphics Interface to the BrookhavenProtein Data Bank, Nature , Vol. 374, pp. 572-574(1995).

[9] M. C. Peitsch, D. R. Stampf, T. N. C. Wells, and J. L.Sussman, The Swiss 3D-Image Collection andBrookhaven Protein Data Bank Browser on the World-Wide Web, TIBS, Vol. 20, pp. 82-84 (1995).

[10] A. Bairoch and B. Boeckmann, The SWISS-PROTProtein Sequence Data Bank: Current Status, Nucl.Acids Res., Vol. 22, pp. 3578-3580 (1994). URL:http://expasy.hcuge.ch/sprot/sprot-top.html.

[11] B. R. Seavey, E. A. Farr, W. M. Westler, and J. L. Markley,A relational database for sequence-specific proteinNMR data, J. Biomol. NMR Vol. 1, pp. 217-236 (1991).URL: http://www.bmrb.wisc.edu

[12] A. Bairoch, The ENZYME Data Bank, Nucl. Acids Res.,Vol. 22, pp. 3626-3627 (1994).

[13] Entrez [on-line and CD-ROM]. National Center forBiotechnology Information, National Library ofMedicine, National Institutes of Health, Bethesda, MDU S A ( p r o d u c e r ) . A v a i l a b l e U R L :http://www3.ncbi.nlm.nih.gov/Entrez.

[14] I. A. Chen, and V. M. Markowitz, An overview of theObject-Protocol Model (OPM) and OPM datamanagement tools, Information Systems Vol. 20 (5),393-418 (1995). (Article and related informationa v a i l a b l e a t U R L :http://gizmo.lbl.gov/DM_TOOLS/OPM/opm.html).

[15] K. H. Fasman, A. J. Cuticchia, and D. T. Kingsbury, TheGDB Human Genome Data Base anno 1994, Nucl. AcidsRes., Vol. 22, pp. 3462-3469 (1994).

[16] K. E. Sidman, D. G. George, W. C. Barker, and L. T. Hunt,The Protein Identification Resource (PIR), Nucl. AcidsRes., Vol. 16, pp. 1869-1871 (1988).

[17] D. G. George, W. C. Barker, H. W. Mewes, F. Pfeiffer, andA. Tsugita, The PIR - International Protein SequenceDatabase, Nucl. Acids Res., Vol. 22, pp. 3569-3573(1994).

[18] A. Bairoch and P. Bucher, PROSITE: RecentDevelopments, Nucl. Acids Res., Vol. 22, pp. 3583-3589(1994). URL: http://expasy.hcuge.ch/

[19] S. Henikoff and J. G. Henikoff, Protein familyclassification based on searching a database of blocks,G e n o m i c s Vol. 19, pp. 97-107 (1994). URL:http://blocks.fhcrc.org/

[20] W. R. Pearson and D. J. Lipman, Improved tools forbiological sequence comparison, Proc. Natl. Acad. Sci.USA Vol 85, pp. 2444-2448 (1988).

[21] S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J.Lipman, Basic local alignment search tool, J. Mol. Biol.Vol. 215, pp. 403-410 (1990).

[22] National Center for Biotechnology Information,National Library of Medicine, National Institutes ofHealth, Bethesda, MD USA (producer). Available URL:http://www.ncbi.nih.gov. Available anonymous FTP:ncbi.nlm.nih.gov. Directory: /repository/taxonomies.

[23] Biochemical Nomenclature and Related Documents, acompendium, second edition, International Union ofBiochemistry and Molecular Biology, prepared byClaude Liebecq, Portland Press Ltd., London (1992).

[24] MEDLINE [on-line and CD-ROM]. National Library ofMedicine, National Institutes of Health, Bethesda, MDUSA (producer). Available: NLM, DIALOG, BRS,SilverPlatter.

[25] K. Nishikawa, S. Ishino, H. Takenaka, N. Norioka, T.Hirai, T. Yao, and Y. Seto, Constructing a proteinmutant database, Protein Eng. Vol. 7, pg. 733 (1994).

[26] F. H. Allen, J. E. Davies, J. J. Galloy, O. Johnson, O.Kennard, C. F. Macrae, E. M. Mitchell, G. F. Mitchell, J.M. Smith, and D. G. Watson, The development ofversions 3 and 4 of the Cambridge Structural DatabaseSystem, Journal of Chemical Information andComputer Science Vol. 31, pp. 187-204 (1991).

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7. Appendix A: Description of primarydatabase objects

The following describe two primary object classes foundin 3DBase. For a more complete and detailed view, youmay use our schema browser at URLhttp://pdb.pdb.bnl.gov/opmbrowser.html. An OPMschema consists of definitions of object classes, eachdescribed by a set of attributes. Data types assigned toattributes can be primitive types such as numbers orcharacter strings, or they can be other classes defined inthe schema. In addition to object classes, OPM providescontrolled value classes that restrict values possible forobjects in the class. Attributes can be either single ormultiple valued. The latter can be specified as an orderedlist (list-of) or as an unordered list (set-of). Object classesare grouped into a hierarchy of subclasses and superclassrelationships called an ISA hierarchy. A class is said toinherit all the attributes of its superclass. In thedescription below object classes have been assigned nameswhich start with the small letter "o", attributes with the

small letter "a", and controlled value classes with theprefix "cv".

oExperimentisa o3DBExportObj

*aTitle: list-of varchar(255)requiredDescription: Contains a title for the experiment oranalysis that is represented in the object. It shouldidentify an entry in the PDB in the same way that a titleidentifies a paper.*aDepositor: list-of oPersonrequiredDescription: An ordered list of names with addressinformation.*aKeywords: set-of varchar(80)optionalDescription: Set of keywords relevant to the entry. Theseprovide a simple means of categorizing the experiment orthe molecules studied.*aExpdta: cvExperimentTypesrequiredDescription: Identifies the experimental technique used inthe study. This normally refers to the type of radiationand sample, but can also include the spectroscopic ormodeling technique. Permitted values include:

ELECTRON DIFFRACTIONFIBER DIFFRACTIONFLUORESCENCE TRANSFERNEUTRON DIFFRACTIONNMRTHEORETICAL MODELX-RAY DIFFRACTION

*aReference: list-of oExternalReferenceoptionalDescription: Publications related to the study. Thesecitations are chosen by the depositor.*aRemarks: set-of oAnnotationsoptionalDescription: General comments regarding the experimentor the molecules studied.

oMacroMoleculeisa o3DBExportObj

*a3DBID: char(4)requiredDescription: Contains the PDB identification code. Thisis a four character field of which the first character must bean integer greater than zero. This identifier is uniquewithin PDB and is assigned randomly to an entry.*aMolName: set-of varchar(80)optionalDescription: Set of molecule names. Each molecule maybe assigned more than one name allowing for the use ofsynonyms and aliases.

*aSrcDescr: oSourceoptionalDescription: Specifies the biological and/or chemicalsource of each biological molecule in the entry. Sourcesare described by both the common name and scientificnames, genus and species. Strain and/or cell-line forimmortalized cells are given when they help in uniquelyidentifying the biological entity studied.*aMolType: cvMacroMoleculeTypeoptionalDescription: Molecule type -Valid values are:

proteinDNA

RNApolysaccharideother - must annotate

*aBioMol: varchar(255)optionalDescription: Information on accessing the structure of thecomplete biological molecule. Currently this contains thefilename for a biomol entry found in the PDB ftp server.This attribute will be replaced by a new object class withattributes that provide the transformation matrices,descriptive text, and, if available, the filename for thecoordinate set.*aCoordinates: set-of oChainoptionalDescription: Atomic coordinate values stored asindividual chains.*aMolSequence: list-of oPrimarySeqoptionalDescription: SEQRES records contain the amino ornucleic acid sequence of residues in each chain of themacromolecule.*aDomain: varchar(100)optionalDescription: Specifies a domain or region of the molecule.*aEngineered: cvFlagDictoptional*aEnzyme: set-of oExternalReferenceoptionalDescription: The Enzyme Commission number associatedwith the molecule.*aMutation: varchar(255)optionalDescribes the mutations present.*aFormula: varchar(80)optional*aMolWeight: floatoptional*aMolID: cvLocalIDrequiredDescription: Integer to uniquely identify each instance of acoordinate set for a molecule. For example, eachoccurrence of lysozyme in the database will be identifiedby a unique number.*aAnnotate (aSummLine, aExtDB) :

set-of (varchar(255), oExternalReference)

optionalDescription: Annotations describing the molecule. This ispresented as a table of text and pointer to an externaldatabase.

8. Appendix B: 3DBase Report inDifferent Formats

3DBase - raw formatFor the oMacromolecule object of the entry 1ACE:*Export_Object: 1ACE*Macromol_name: Acetylcholinesterase*Macromol_name: Ache*EC_number: 3.1.1.7*3DB_init_res_num: 4*3DB_term_res_num: 534*Init_res_num: 25*Term_res_num: 555*Database_ID_code: ACES_TORCA*Domain_desc: No*Engineered: No*Source_sci_name: Torpedo californica*Source_common_name: Pacific electric eel

Data in BoulderIO format:

Export_Object = 1ACEMacromol_name = AcetylcholinesteraseMacromol_name = AcheEC_number = 3.1.1.7Chain = {

3DB_init_res_num = 43DB_term_res_num = 534

Init_res_num = 25Term_res_num = 555Database_ID_code = ACES_TORCA

}Domain_desc = NoEngineered = NoSource_sci_name = Torpedo californicaSource_common_name = Pacific electric eel

9. Appendix C: Guided Tour to 3DBBrowser

• Search for "acetylcholinesterase" where Kinemageannotation is available

• Search for "epidermal" into NMR experimental data

10. Appendix D: Guided Tour to AutoDep

10.1 Introduction

This is a description of how to submit data to the PDBusing AutoDep. If you have made submissions to thePDB before, then the WWW AutoDep form is a lot likethe earlier Electronic Deposition Form with the followingadditional features:

• You can start with an existing PDB entry or apreviously completed Deposition Form.

• Your deposition is partially verified as youcomplete it, saving a lot of time: we catch errorswhile you are still available to correct them.

• We provide a script that downloads all of therequired data to the PDB (Unix only).

• As you are already using the Web, hot links areprovided that may be useful in constructing yoursubmission.

10.2 Overview of the Process

1) Select a location for your submission. We are pleasedto have global partners in Israel and the United Kingdomthat will soon be serving as deposition sites. Sometimes,the speed of network links would dictate the use of onesite over another.2) The next step concerns security and confidentiality. Weprovide you with a deposition number consisting of threeletters, a dash, and a number, and ask you to provide apassword. Anyone who knows both the deposition codeand the password has access to your deposition. Thisallows you to make future submissions based on earlierones. If you prefer us to block all access at the completionof the deposition process, please instruct us accordingly.This may be done in the section entitled "SpecialInstructions" to the PDB. As a security measure, if aspecific amount of time has passed between transactions,or the request comes from a different computer, you willbe asked to re-enter the password. The number of timesyou should have to do this will be minimal, but it isdone to protect against an unmonitored workstation beingused to view your work.

3) The next step is to transfer to the PDB AutoDep servervarious data files that are needed to initiate the AutoDepprocess. This is done by:

• Selecting and filling in the section "Files BeingDeposited".

• Among the files you may need to transfer are:PDB-formatted output data from an X-rayrefinement program such as X-PLOR, SHELX,etc., or a PDB file containing your coordinates;topology, parameter, restraints, sequence andalignment files, etc.

• You will be given a Unix script which you maycopy and paste into a shell or X window with yourmouse: run this script to transfer the files. Pleasenote that a bug exists in the SGI operating systemthat precludes you from using this script in aWINTERM window running tcsh. In that case, youwill have to open an xterm window or run csh inone of the standard windows.

• Reload the Main Menu Page and click on themerge button to enter the data into the DepositionForm, overwriting anything already existing inthose fields.

4) Next, you will be asked to complete the remainingsections.5) You may preview the PDB file at any time during theprocess in order to view how it is shaping up.6) You may also view the dep form and save a completedcopy of it for your records.7) Within seconds of your submission, you will be sentan e-mail acknowledgement that your submission hasbeen received at the PDB.8) If the coordinates pass the syntax check you willreceive your PDB ID code within seconds. If not you willbe asked to make corrections to the format and resubmityour deposition.

So - Let's Begin!

To which location do you prefer to submit your data?

• Brookhaven National Laboratory, New York State,USA

• Weizmann Institute of Science, Rehovot, Israel• EMBL Outstation, European Bioinformatics

Institute, Hinxton, United Kingdom

Figures for Appendix C: Guided Tour to 3DB Browser

Figures for Appendix D: Guided Tour to AutoDep