The Protein Data Bank:
current status and future challenges

Joel L. Sussman1,2, Enrique E. Abola1, Nancy O. Manning1, Jaime Prilusky3

1 Protein Data Bank, Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000, USA
2 Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
3 Bioinformatics Unit, Weizmann Institute of Science, Rehovot 76100, Israel


  1. Introduction
  2. Resource Status, July 1996
  3. The 3-Dimensional Datatabase of Biomacromolecules Structures (3DB)
    • 3.1 The 3DBase - A Relational Database Management System for 3DB
    • 3.2 Schema Development
    • 3.3 Building Semantic Links to External Data Sources
  4. Data Deposition
    • 4.1 Current Data Deposition Procedures
    • 4.2 Development of Automatic Deposition and Validation
    • 4.3 AutoDep's most important features
  5. Accessing data in 3DBase
  6. Appendix A: Description of primary database objects
  7. Appendix B: 3DBase Report in different formats
  8. Appendix B: Guided tour to 3DB browser
  9. Appendix C: Guided tour to AutoDep
  10. References

1. Introduction

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

The challenge facing the new 3DB is to keep abreast of the increasing flow of data, to maintain the archive as error-free as possible, and to organize and present this information in ways that facilitate data retrieval, knowledge exploration, and hypothesis testing without interrupting current services. The PDB introduced substantial enhancements to both data management and archive access in the past two years, and is well on the way to converting to a more powerful system that combines the advantages of object oriented and relational database systems. 3DB will transform PDB from a Data Bank serving solely as a data repository into a highly sophisticated knowledge-based system for archiving and accessing structural information. The process will be evolutionary, insulating users from drastic changes and providing both a high degree of compatibility with existing software and a consistent user interface for casual browsers.

Development is underway for 3DB to operate as a direct-deposition archive, providing mechanisms for depositors to submit data over the Internet with minimal staff intervention. Data archived in 3DB is managed using the Relational Database Management System (RDBMS), SYBASE [4]. The new database (3DBase) is being developed with a view towards being a member of a federation of biological databases. Collaborative international centers are also being established to assist in data deposition, archiving, and distribution activities.

2. Resource status, July 1996

Rapid developments in preparation of crystals of macromolecules and in experimental techniques for structure analysis and refinement have led to a revolution in Structural Biology. These factors have contributed significantly to an enormous increase in the number of laboratories performing structural studies of macromolecules to atomic resolution and the number of such studies per lab. Advances include: 1) recombinant DNA techniques that permit almost any protein or nucleic acid to be produced in large amounts; 2) better X-ray detectors; 3) real-time interactive computer graphics systems, together with more automated methods for structure determination and refinement; 4) synchrotron radiation, 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 of macromolecules in solution; and 6) electron microscopy (EM) techniques, for obtaining high-resolution structures.

[PDB coordinate entries available]

Fig 1. PDB Coordinate Entries Available

These dramatic advances produced an abrupt transition from the linear growth of 15-25 new structures deposited per year in the PDB before 1987 to a rapid exponential growth reaching the current rate of ~25 deposits per week (Fig. 1). This rapid increase overwhelmed PDB staff resources and data processing procedures and, by mid-1993, a backlog of some 800 coordinate entries had accumulated. This backlog was eliminated by January 1994 by increasing automation of processing and hiring additional staff. In all, more than 3,500 of the ~4,600 current PDB coordinate entries (~75%) have been processed since 1991. Table 1 is a summary of the contents of PDB. Present staff now keep abreast of the deposition rate with a timeline of three months from receipt to final archiving, which includes the time that the entry is with the depositor for checking. This timeline is comparable to the publication schedules of the fastest scientific journals.

PDB Archive Contents
4652released atomic coordinate entries
576structure factor files
169NMR restraint files
Molecule type
4207proteins, peptides, and viruses
108protein/nucleic acid complexes
325nucleic acids
12carbohydrates
Experimental Technique
3865diffraction and other
651NMR
136theoretical modeling

Table 1. PDB Archive Contents - July 1996

In the same period, the proliferation and increasing power of computers, the introduction of relatively inexpensive interactive graphics, and the growth of computer networks greatly increased the demand for access to PDB data (Fig. 2). The requirements of molecular biologists, drug designers, and others in academia and industry are often fundamentally different from those of crystallographers and computational chemists, who have been the major users of the PDB since the 1970's.

[FTP data access]

Fig 2. FTP data access


PDB entries are available on CD-ROM, which PC 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 the molecular viewing program RasMol [7]. They are also accessible on the Internet via a World Wide Web (WWW) browser, PDBBrowse [8] at Brookhaven and several mirror sites worldwide.

The PDBBrowse incorporates a number of features that make it easy to access information found in PDB entries. Multiple search strings covering various fields, corresponding to PDB record types such as compound, header, author, biological source, or heterogen data, are supported. These searches support boolean 'and', 'or', and 'not' operators. Entries selected can be retrieved automatically, and the molecular structures can be displayed using the public-domain X-based molecular viewer RasMol (or similar viewer). They also include hypertext links to SWISS-PROT [10], BMRB [11], the Enzyme Commission Database, and the Entrez Reference Database [13]. Internet access to the archives has become the primary mode of retrieving entries from the PDB. However, we continue to receive a considerable number of orders for our CD- ROM product. We anticipate that this will continue to be true for a variety of reasons. For example, network performance still remains poor in a number of locations and these disks, released quarterly, provide local access to the contents of the archive. Some of these network access difficulties are easily overcome by installing a copy of the PDB FTP and WWW servers using mirroring software. With this software all files in the PDB are stored locally and any changes are automatically reflected on a daily basis.

3. The 3-dimensional database of biomacromolecules structures (3DB)

Implementing plans to convert PDB to 3DB entails changes to every aspect of current operations. A new data submission and archival system is being implemented which attempts to balance the need for full automation with the need to maintain very high levels of data accuracy and reliability. The new system relies on an RDBMS for data management and archival. An overview of the relationships between 3DBase and depositors, users, third party software developers, and other databases is shown in Fig. 3. The following sections gives a summary of development work.

[3DBase relationships]

Fig 3. 3DBase relationships.

3.1 The 3DBase - a relational database management system for 3DB

The 3DBase is constructed with the SYBASE RDBMS, the Object-Protocol Model (OPM), and the OPM data management tools [14] developed by Victor Markowitz's group at Lawrence Berkeley National Laboratory. SYBASE provides a powerful and robust environment for data management, the OPM tools allow rapid development of SYBASE databases, while OPM's object-oriented view provides a scientifically intuitive representation of data. Along with a graphical schema editor, Markowitz's group distributes a number of other development tools, foremost is a schema translator that generates SQL statements for building tables, indices, constraint rules and triggers.

This development effort attempts to address the needs of the diverse user community served by the PDB. The schema supports queries by those interested in answering crystallographic questions as well as molecular biology questions. The system is being designed with the idea that it will shortly be federated with other biological databases. Our expectation is that through federation, complex queries may be submitted to our database, for which answers that traverse several databases may be easily returned. Interoperability is addressed through the use of schema sharing with other OPM-based databases and support for a variety of data interchange formats in the query results. In addition to providing users with a powerful environment to do complex ad-hoc queries, 3DBase will also facilitate managing the growing archive, which is expected to contain over 30,000 structural reports by the year 2000.

This work is being done as a collaboration among the following groups:

3.2 Schema development

OPM is a semantic data model that includes constructs which are powerful enough to represent the diversity and complexity of data found in PDB entries. OPM has constructs such as object class, object attribute, class hierarchy and inheritance, and derived attribute. A schema for 3DBase has been developed using OPM and is available for perusal through the PDB WWW home page. Among its notable features is a description of the coordinate data set from two perspectives. The object class oExperiment provides users with the classical view of a PDB entry which is a report of crystallographic or NMR analysis. An alternative view is presented in the class oMacroMolecule that describes the biologically active form of the molecule. Appendix A provides a description of these object classes. A clear example which demonstrates the differences in these classes is the case of the hemoglobin molecule. The oExperiment object contains the coordinates for the crystallographic asymmetric unit, which in most cases is a dimer. The full tetramer will however be presented in the oMacroMolecule object. The latter case is normally what molecular biologists are interested in when accessing PDB entries. However, crystallographers wishing to do packing studies or further refinement will need access to the oExperiment object.

In 3DBase, literature citation data are being loaded into the CitDB database of references that was developed by GDB [15]. A pointer to the appropriate entry in CitDB is loaded in the oExperiment object of 3DBase. This is an example of the strategy that we are following in linking to external databases. CitDB will be managed as a federation run by a number of database centers that includes GDB and PDB. There are several advantages to this scenario. By sharing the schema and management of the citation database, access to information stored in each of the database via the bibliographic citation becomes straightforward. Duplication of effort is also minimized. Today it is still common to have several public databases build and maintain their own bibliographic databases. This will no longer be economically feasible with the expected rapid growth in database size.

3.3 Building semantic links to external data sources

Links to contents of sequence databases are provided in 3DBase via the oPrimarySeq and oSeqAdv classes. These classes form another set of objects that link 3DBase objects to external databases. Representing, building, and maintaining these links will be one of 3DB's primary task in the coming years. There are several issues that must be addressed for this effort to succeed. Data representation issues are foremost. Each database use different data models to represent and store information. Semantic contents are rarely the same, for example the primary sequence data stored in sequence databases such as SWISS-PROT or PIR [16, 17] are presented using a view which differs significantly from that used by PDB.

In general PIR and SWISS-PROT entries contain information on the naturally-occurring wild-type molecules. Each entry normally contains the sequence of one gene product and some entries include the complete precursor sequence. Annotation is provided to describe residue modifications. In both databases, the residue names used are limited to the 20 standard amino acids.

In contrast, PDB entries contain multichain molecules with sequences that may be wild type, variant, or synthetic. Sequences may also have been modified through protein engineering experiments. A number of PDB entries report structures of domains cleaved from larger molecules.

The oPrimarySeq object class was designed to account for these differences by providing explicit correlations between contiguous segments of sequences as given in PDB ATOM records and PIR or SWISS-PROT entries. Several cases are easily represented using this class. Molecules containing heteropolymers will be linked to different sequence database entries. In some cases, such as those PDB entries containing immunoglobulin Fab fragments, each PDB chain may be linked to several different SWISS-PROT entries.

This facility is needed, because these databases represent sequences for the various immunoglobulin domains as separate entries. oPrirmarySeq should also be able to represent molecules engineered by altering the gene (fusing genes, altering sequences, creating chimeras, or circularly permuting sequences). In addition it will also be possible to link segments of the structure to entries in motif databases (e.g. PROSITE [18], BLOCKS [19]) .

Initial building of these links is straightforward and requires analysis of a few entries coming out of a FASTA or BLAST search against the sequence databases. What may be problematic in the long run is updating these links as new experimental evidences is encountered, leading to a correction in either database. Both PIR and SWISS-PROT have similar problems as they build pointers to PDB entries. To help obviate these difficulties we have agreed to establish a closer interaction between the databases. We are setting up a protocol that will broadcast to each database changes that occur which in turn could affect specific entries.

4. Data deposition

3DB will operate as a direct-deposition archive, providing mechanisms that will allow depositors to load data with minimal staff intervention. This strategy is essential if 3DB is to meet present projections of exponential growth in depositions against a fixed staff size. This is particularly challenging, due to the complexity of the data being handled, the need for a common viewpoint of the entry description, and the community requirement that these data be accessible immediately upon receipt.

With direct deposition, there will be a concomitant need to increase the power of data validation procedures. These procedures must reflect current models for identifying errors and must be as complete as possible. Quality control issues assume a more central and difficult role in direct deposition strategies. Distributed data must be of the highest quality; otherwise users will lose their trust in the archived data and will have to revalidate data received from 3DB before using them, clearly an unproductive scenario.

4.1 Current data deposition procedures

Since its inception in 1971, the method followed by the PDB for entering and distributing information paralleled the review and edit mode used by scientific journals. Currently, the author submits information which is converted into a PDB entry and run against PDB validation programs by a PDB processor. The entry and the output of the validation suite are then evaluated by a PDB scientific staff member, who completes the annotations and returns the entry to the author for comment and approval. Table 2 summarizes checks included in our current data validation suite. Corrections from the author are incorporated into the entry, which is reanalyzed and validated before being archived and released.

ClassWhat is checked
stereochemistrybond distances and angles Ramachandran plot (dihedral angles) planarity of groups chirality
bonded/non-bonded interactionscrystal packing, unspecified inter- and intraresidue links
crystallographic informationMatthews coefficient, Z-value, cell transformation matrices
noncrystallographic transformationvalidity of noncrystallographic symmetry
primary sequence datadiscrepancies with sequence databases
secondary structuregenerated automatically or visually checked
heterogen groupsidentification, geometry and nomenclature
miscellaneous checkssolvent molecules outside the hydration sphere, syntax checks, internal data consistency checks

Table 2. Data validation with current system

Originally data flow was a manual system, designed for a staff of 1-2 scientists, and a deposition rate of about 25-50 entries per year. One person processed an entry from submission through release. By the late 1980's, when the first steps at automation were being introduced, running the validation programs took about 4 hours per entry. Today, the same step, which includes a vastly improved set of validation programs, takes about one minute. Graphical viewing of data, a useful and powerful annotating and checking tool, has been available to processors since 1992.

The current deposition load of ~100 entries a month is handled by about ten staff members, who annotate and validate entries. The process is a production line in which checking is repeated at various steps to ensure that errors and inconsistencies in data representation are minimized. Prior to June 1994, a significant number of depositions required that administrative staff keyboard information provided in a deposition form. Introduction of the current Electronic Deposition Form and a new parsing program has greatly reduced, though still not yet completely eliminated, hand entry of information into entries.

Today, most of the processing time is spent resolving data representation issues and ensuring that outliers are identified and annotated. The most troublesome areas consistently are those involving handling of heterogens, resolving crystal packing issues, representing molecules with non-crystallographic symmetry, and resolving conflicts between the submitted amino acid sequence and that found in the sequence databases. Publications and other references are sometimes consulted to verify factual information such as crystal data, biological details, reference information, etc. Processing programs, although much improved from those used in 1991, still allow errors to pass undetected through the system, requiring a visual check of all entries. We continually improve these programs and acquire software from collaborators to address deficiencies that both we and our users have identified. In addition, we now have formed a quality control group that will be looking into our operations to identify sources of errors and to recommend steps to improve data quality.

4.2 Development of automatic deposition and validation

3DB must overcome many challenges for direct deposition to work. In a recent workshop held to assess the needs of 3DB users, crystallographers and NMR spectroscopists were unanimous in their desire to have a system that did not require additional work on their part when depositing data. On the other hand, consumers (which included these same depositors) were vocal in their desire for entries to contain more information than what is currently available within the PDB. We are striving to develop a suite of deposition and validation programs that accommodates these somewhat conflicting desires while ensuring that the archives maintain the highest standard of accuracy. A schematic of the automatic deposition process is depicted in Fig. 4.

[3DBase automatic validation]

Fig 4. 3DBase automatic validation.

A considerable variety of information is archived about each structure which must be supplied by the authors. The AutoDep program, currently under development, is expected to simplify the deposition process. It includes a convenient and interactive electronic deposition protocol that guides the author in providing information. It also contains tools for data verification and validation and is able to flags errors in syntax or spelling. The form requests approximately 500 items, including a description of the experiment and the molecule under study. Steps are being taken to help ease the burden of filling out this form. For example, the program can fill in fields using data from an existing PDB entry. These data can then be modified to reflect the contents of the new deposition. Checks against other databases are an important and evolving part of this process. For example, names of organisms are checked against the taxonomy database of the National Center for Biotechnology Information (NCBI) [22] , chemical names against IUPAC [23] nomenclature tables, and author names and citations against MEDLINE [24] (CitDB when it becomes available). FASTA/blast programs are run against the SWISS-PROT and PIR databases to verify protein sequences, and variant and mutant sequences are checked against the Protein Mutant Database [25] (PMD). Links between the PDB/3DB entry and these databases are established in the process. To handle the increasing number of entries with nonstandard residues (heterogens), a standard residue and heterogen dictionary is being developed to be used in the data entry and checking process. We are also adopting programs developed by the Cambridge Crystallographic Data Center [26] (CCDC) and elsewere to handle heterogens automatically for use in AutoDep.

In addition to the deposition form that is filled out by AutoDep, authors are requested to submit the coordinate data entry and other experimental data files for processing and archive. Facilities are provided by AutoDep that help simplify this process. An FTP script is provided that author specified local filenames uploads to the PDB server site.

The completed form is then converted automatically into a file in PDB format, and along with the coordinate data are submitted to a set of validation programs for checking and further annotation. These programs are designed to check 1) the quality, consistency, and completeness of the experimental data, 2) possible violations of physical or stereochemical constraints (e.g., no two atoms in the same place, appropriate bond angles, etc.), 3) compliance with our data dictionary (syntax checks) and 4) in the near future, the correspondence of the experimental data to the derived structure. Development of the validation suite will evolve with advice from the community and encompass programs currently in use, written both within and outside PDB.

The validation software automatically generates and includes in the entry measures of data quality and consistency, as well as annotations giving details of apparent inconsistencies and outliers from normal values. This output is returned to the depositor for review. Entries whose data quality and consistency meet appropriate standards may then be sent by the depositor directly for automatic entry into the database. Entries that do not pass the quality and consistency checks may be revised by the depositor to correct for inadvertent errors, or alternatively, more experimental work may be needed to resolve problems uncovered.

Apparent inconsistencies or outliers may remain in a submitted entry, provided these are explained by the depositor in an annotation. In the most interesting cases, unusual features are a valid and important part of the structure. However, all such entries will be reviewed for possible errors by 3DB staff, who may discuss any important issues with the depositor. 3DB staff will then forward acceptable entries to the database.

To make automatic deposition as easy as possible, we are working with developers of software commonly used by our depositors. By modifying these programs to produce compliant data files and performing validation and consistency checks before submission, it may be possible to bypass most of the tedious steps in deposition. We are already working with Dr. A. Br&uumlnger to use procedures available through X-PLOR [27] to replace part of the validation suite for structures produced by X-ray crystallography and NMR. Diagnostic output will be included automatically as annotations in the entry. A limited version of X-PLOR will be available from BNL to all depositors for validation purposes only.

Validation of coordinate data against experimental X-ray crystallographic data requires access to structure factor data, which are requested by PDB, the International Union of Crystallography (IUCr) and some journals but are not always supplied by the depositor. We are working toward building consensus in the community that structure factor data are a necessary component of deposits 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 in the 3DB entry as annotation for the experiment.

In order to make it easier for depositors to submit structure factors (as well as to exchange these data between laboratories), the PDB , in close collaboration with a number of macromolecular crystallographers has developed a standard interchange format for these data. This standard is in CIF (Crystallographic Information File) [29, 30] and was chosen both for simplicity of design and for being clearly self-defining, i.e. that the file contains sufficient information for the file to be read and understood by either a program or a person. Details of this format is available through the PDB WWW server.

A consensus is still developing in the NMR community as to what types of experimental data should be deposited and what kinds of validation and consistency checks should be performed. Structural data produced by other methods may also have special features that should be archived or checked, for example the sequence alignment used for modelling studies. Requirements for the types of data to be deposited and proper ways of checking the validity and consistency of the data will be developed in cooperation with the experimental community for each type of structure data archived by the 3DB.

4.3 AutoDep's most important features

  • The ability to fill in the form automatically from an existing PDB entry or a previous deposition. As easy as pushing a button, AutoDep will enter data from the designated file to the appropriate fields in the new form. The author merely has to update fields to reflect the new structure.

  • X-Ray structural refinement software is available to write PDB records that can be automatically merged into the deposition form. For example, the new releases of X-PLOR [27] and SHELX-96 write refinement details as PDB records which will be read by the program and entered in the relevant sections. We are continuing to work with authors of various programs and anticipate that increasing numbers of programs will be integrated with PDB.

  • Each session has help files, examples, and links to related documentation and useful URLs in each section to support the author during the AutoDep session.

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

  • The AutoDep session can be interrupted at any time and returned to hours, days, or even weeks later. The session id number and password must be recorded to continue with the same deposition.

  • When an author is satisfied with the completed deposition form, a script is provided which allows cutting and pasting to your local computer to automatically download the completed form and all associated files to the PDB.

5. Accessing data in 3DBase

User queries and report generation access to 3DBase will be via the network using general purpose graphical user interfaces like Mosaic or Netscape. Access will also be available through the use of software developed by third parties (commercial developers). As diagrammed in Fig. 5, user queries will be addressed to the Query Analyzer (3DB-QA), a program module running at the server site that will parse queries and pass them on to 3DBase. Query results will be returned through the Output Generator (3DB-OG) in the format requested by the user. Queries placed over the network will generally be in the form of URLs, which are easily generated from HyperText links, HTML-based forms, or by programs or scripts using the National Center for Supercomputing Applications libraries [28] for more sophisticated applications. As part of the query the user may specify the format of the response, as we do at the present time in the PDB WWW browser. The response frequently will be in the form of an HTML document, but it can also be a PDB- or CIF-formatted file [29 , 30] . The information returned may be either a complete or partial entry, and may include information from linked databases or external programs.

[accessing 3DBase]

Fig 5. Accessing 3DBase.

A 3DBase browser has been built using Stan Letovsky's Genera system. Users specify search criteria by filling out an HTML form. Software at BNL processes this form and generates the required SQL. System performance is improved by using stored SYBASE SQL procedures that access each predefined object. The fields available are similar to those in our PDBBrowse program and answer most of the questions that users have been asking.

For those familiar with (or willing to learn about) the OPM protocol, access to the object layer will be provided using a high level OPM-based query language. As part of the 3DB open database policy, direct access to the underlying RDBMS will be allowed and actively supported. These queries are not parsed by the 3DB-QA module, so better response time can be expected. This provides third party developers with the opportunity to either incorporate SQL clients in their products or to learn more of the OPM protocol and thereby gain access to all of the benefits that the Object model affords (e.g., active external links, programs, etc.). As depicted in figure 5, the output generator will return query results using a variety of data interchange formats. PDB will continue to support its current format in the foreseeable future. We also plan to extend this format to allow us to represent objects being stored in 3DBase. In addition, a "raw format" is being provided which returns an attribute/value pair. This form is easily parsed and is more compact than the PDB format.

6. Appendix A: Description of primary database objects

The following describe two primary object classes found in 3DBase. For a more complete and detailed view, you may use our schema browser at URL http://pdb.pdb.bnl.gov/opmbrowser.html. OPM schema consists of definitions of object classes, each described by a set of attributes. Datatypes assigned to attributes can be primitive types such as numbers or character strings, or they can be other classes defined in the schema. In addition to object classes, OPM provides controlled value classes which restricts values possible for objects in the class. Attributes can be either single or mulitple valued. The latter can be speficied as an ordered list (list-of) or as an unordered list (set-of). Object classes are grouped into a hierarchy of subclasses and superclass relationship called an ISA hierarchy. A class is said to inherit all the attributes of its superclass. In the description below object classes have been assigned name which start with the small letter "o", attributes with the small letter "a", and controlled value classes with the prefix "cv".

oExperiment
isa o3DBExportObj

*aTitle: list-of varchar(255)
required
Description: Contains a title for the experiment or analysis that is represented in the
object. It should identify an entry in the PDB in the same way that a title identifies a
paper.
*aDepositor: list-of oPerson
required
Description: An ordered list of names with address information
*aKeywords: set-of varchar(80)
optional
Description: Set of keywords relevant to the entry. These provide a simple means of
categorizing the experiment or the molecules studied.
*aExpdta: cvExperimentTypes
required
Description: Identifies the experimental technique used in the study. This normally refers
to the type of radiation and sample, but can also include the spectroscopic or
modeling technique. Permitted values include:

ELECTRON DIFFRACTION
FIBER DIFFRACTION
FLUORESCENCE TRANSFER
NEUTRON DIFFRACTION
NMR
THEORETICAL MODEL
X-RAY DIFFRACTION
*aReference: list-of oExternalReference
optional
Description: Publications related to the study. These citations are chosen by the
depositor.
*aRemarks: set-of oAnnotations
optional
Description: General comments regarding the experiment or the molecules studied.

oMacroMolecule
isa o3DBExportObj

*a3DBID: char(4)
required
Description: Contains the PDB identification code. This is a four character field of which
the first character must be an integer greater than zero. This identifier is unique
within PDB and is assigned randomly to an entry
*aMolName: set-of varchar(80)
optional
Description: Set of molecule names. Each molecule may be assigned more that one
name allowing for the use of synonyms and aliases.
*aSrcDescr: oSource
optional
Description: Specifies the biological and/or chemical source of each biological molecule
in the entry. Sources are described by both the common name and scientific names,
genus and species. Strain and/or cell-line for immortalized cells are given when they
help in uniquely identifying the biological entity studied.
*aMolType: cvMacroMoleculeType
optional
Description: Molecule type -Valid values are:
protein
dna
rna
polysaccharide
other - must annotate
*aBioMol: varchar(255)
optional
Description: Information on accessing the structure of the complete biological molecule.
Currently this contains the filename for a biomol entry found in the PDB ftp server.
This attribute will be replaced by a new object class with attributes that provide the
transformation matrices, descriptive text, and if available the filename for the
coordinate set.
*aCoordinates: set-of oChain
optional
Description: Atomic coordinate values stored as individual chains
*aMolSequence: list-of oPrimarySeq
optional
Description SEQRES records contain the amino or nucleic acid sequence of residues
in each chain of the macromolecule.
*aDomain: varchar(100)
optional
Description: Specifies a domain or region of the molecule
*aEngineered: cvFlagDict
optional
*aEnzyme: set-of oExternalReference
optional
Description: The Enzyme Commission number associated with the molecule
*aMutation: varchar(255)
optional
Describes the mutations present
*aFormula: varchar(80)
optional
*aMolWeight: float
optional
*aMolID: cvLocalID
required
Description: Integer to uniquely identify each instance of a coordinate set for a molecule.
For example, each occurences of lysozyme in the database will be identified by a
unique number.
*aAnnotate (aSummLine, aExtDB) :
set-of (varchar(255), oExternalReference)
optional
Description:Annotations describing the molecule. This is presented as a table of text and
pointer to an external database.

7. Appendix B: 3DBase Report in different formats

3DBase - raw format
For 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
*Databae_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 = 1ACE
Macromol_name = Acetylcholinesterase
Macromol_name = Ache
EC_number = 3.1.1.7
Chain = {
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

8. Appendix B: Guided tour to 3DB browser


[3DB browser]

[3DB browser]

[3DB browser]

[3DB browser]

[3DB browser]


[3DB browser]

[3DB browser]

[3DB browser]

[3DB browser]




9. Appendix C: Guided tour to AutoDep

Overview of the process

  1. The first step in making a deposition is to select a machine to make the deposition to. Sometimes, the speeds of network links would dictate the use of one machine over another. We are pleased to have our global partners in Israel, Germany and Japan serve as deposition sites. If you don't know which is better, then you can simply use any of them. At worst, it will be a bit sluggish. This choice is made at the bottom of this page.

  2. The next step concerns security and confidentiality. Your deposition is kept in strictest confidence. To make that work with the networks that we have today, we are going to provide you with a deposition code consisting of a three letter code, a dash, and a number, and ask you to provide a password. If there is anyone who knows both the deposition code and the password, they will have full access to the deposition you made. This will allow you to make future depositions based on older depositions, but if you prefer, we will block all access at the completion of the deposition process.

    As a security measure, if a specific amount of time has passed between transactions, or the request comes from a different computer, you will be asked to re-enter the password. The number of times you should have to do this is minimal and it is there to try to protect against an unmonitored workstation being used to view your work. While these measures are NOT fool-proof, they are significantly better than the system in use today. PDB will do everything in its power to maintain the confidentiality of your deposition. You must however do your part as well.

  3. Next, you will be asked to complete a number of simple forms. Nobody likes this step, because it asks many questions. However, the more questions we ask (and the more complete your answers!) the richer the database will be for you and your colleagues. Please take the time to make the best deposition possible.

  4. You may download files to us and use the merge utility to populate the AutoDep form with the PDB-formatted data contained within the file. This will allow users of X-PLOR, SHELX, and a growing number of programs to painlessly enter their data.

  5. Finally, you will be asked to run a script on your machine that transfers all of the data files to the PDB deposition site. At the present time, security concerns dictate that we not try to enable general program execution on your machine. (The scenario is that someone could trick you into deleting all your files, or adding a line to .rhosts, or downloading /etc/password, or all sorts of other devious things.)

  6. You may preview the PDB file at any time during the process in order to view how it is shaping up.

  7. You may also view a the dep form and save a completed copy of it for your records.

  8. You will be sent an e-mail receipt that your submission has been received at the PDB within seconds of your submission.


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10. References

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SYBASE SQL ServerT (UNIX version 10.0) [computer program] (1994). Available Distributor: Sybase Inc., Emeryville, CA USA.
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PDB-SHELL [computer program, on-line and CD-ROM]. Available anonymous FTP: ftp.pdb.bnl.gov.
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MicrosoftR FoxProR Relational Database Management System [computer program]. Available Distributor: Microsoft Corporation, Redmond, Washington 98052-6399 USA.
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R. Sayle, RasMol [computer program]. Available anonymous FTP: ftp.dcs.ed.ac.uk. Directory: /pub/rasmol. File: README [for filenames for different platforms].
[8]
D. R. Stampf, C. E. Felder, and J. L. Sussman, PDBBrowse - a graphics interface to the Brookhaven Protein Data Bank, Nature 374, 572-574 (1995).
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M. C. Peitsch, D. R. Stampf, T. N. C. Wells, and J. L. Sussman, The Swiss-3DImage collection and PDB-Browser on the World-Wide Web, Trends in Biochemical Sciences 20, 82-84 (1995).
[10]
A. Bairoch and B. Boeckmann, The SWISS-PROT protein sequence data bank: current status, Nucleic Acids Res. 22, 3578-3580 (1994). URL: http://expasy.hcuge.ch/sprot/sprot-top.html
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B. R. Seavey, E. A. Farr, W. M. Westler, and J. L. Markley, A relational database for sequence-specific protein NMR data, J. Biomol. NMR 1, 217-236 (1991). URL: http://www.bmrb.wisc.edu
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A. Bairoch, The ENZYME data bank, Nucleic Acids Res. 22, 3626-3627 (1994).
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I. A. Chen, and V. M. Markowitz, An overview of the Object-Protocol Model (OPM) and OPM data management tools, Information Systems 20 (5), 393-418, (1995). (Article and related information available at URL: http://gizmo.lbl.gov/DM_TOOLS/OPM/opm.html).
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K. H. Fasman, A. J. Cuticchia, and D. T. Kingsbury, The GDB Human Genome Data Base anno 1994, Nucleic Acids Res. 22, 3462-3469 (1994).
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K. E. Sidman, D. G. George, W. C. Barker, and L. T. Hunt, The Protein Identification Resource (PIR), Nucleic Acids Res. 16, 1869-1871 (1988).
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D. G. George, W. C. Barker, H. W. Mewes, F. Pfeiffer, and A. Tsugita, The PIR- international protein sequence database, Nucleic Acids Res. 22, 3569-3573 (1994).
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A. Bairoch and P. Bucher, PROSITE: recent developments, Nucleic Acids Res. 22, 3583-3589 (1994). URL: http://expasy.hcuge.ch/
[19]
S. Henikoff and J. G. Henikoff, Protein family classification based on searching a database of blocks, Genomics 19, 97-107 (1994). URL: http://blocks.fhcrc.org/
[20]
W. R. Pearson and D. J. Lipman, Improved tools for biological sequence comparison, Proc. Natl. Acad. Sci. USA 85, 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. 215, 403-410 (1990).
[22]
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 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, a compendium, second edition, International Union of Biochemistry and Molecular Biology, prepared by Claude Liebecq, Portland Press Ltd., London (1992).
[24]
MEDLINE [on-line and CD-ROM]. National Library of Medicine, National Institutes of Health, Bethesda, MD USA (producer). Available: NLM, DIALOG, BRS, SilverPlatter.
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K. Nishikawa, S. Ishino, H. Takenaka, N. Norioka, T. Hirai, T. Yao, and Y. Seto, Constructing a protein mutant database, Protein Eng. 7, 733 (1994).
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[29]
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[31]
S. I. Letovsky, Genera [computer program] (1994). Available URL: http://gdbdoc.gdb.org/letovsky/genera.


Joel L. Sussman
is a macromolecular crystallographer and Head of the Protein Data Bank. He is a Senior Scientist in the Biology Department, Brookhaven National Laboratory, and a Professor in the Department of Structural Biology at the Weizmann Institute of Science.
Joel L. Sussman 
Protein Data Bank Dept. of Structural Biology
Biology Department, Bldg. 463 Weizmann Institute of Science
Brookhaven National Laboratory Rehovot 76100
Upton NY 11973-5000 USA Israel

Phone: (516)-344-6355 972-8-934-2638
Fax: (516)-344-2176 972-8-934-4159
E-mail: csjoel@weizmann.weizmann.ac.il
URL: http://www.weizmann.ac.il/~jsgrp/joel.html

Enrique E. Abola
is a protein crystallographer and is Scientific Coordinator of the Protein Data Bank.
Enrique E. Abola
Protein Data Bank
Biology Department, Bldg. 463
Brookhaven National Laboratory
Upton NY 11973-5000 USA

Phone: (516)-344-6354
Fax: (516)-344-5751
E-mail: abola1@bnl.gov

Nancy O. Manning
is a crystallographer and Coordinator of the Outreach Program of the PDB.
Nancy Oeder Manning
Protein Data Bank
Biology Department, Bldg. 463
Brookhaven National Laboratory
Upton NY 11973-5000 USA

Phone: (516)-344-5744
Fax: (516)-344-5751
E-mail: oeder@bnl.gov
Jaime Prilusky
is Head of PDB's Database Group and is Head of the BioInformatics Unit of the Weizmann Institute of Science.
Dr Jaime Prilusky 
Head Bioinformatics Unit
Dep. of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel

Phone: 972-8-9343456
Fax: 972-8-9344113
E-mail: lsprilus@weizmann.weizmann.ac.il
URL: http://bioinformatics.weizmann.ac.il/jaime_prilusky.html