Enrique E. Abola

Automated analysis of interatomic contacts in proteins.

MOTIVATION New software has been designed to assist the molecular biologist in understanding the structural consequences of modifying a ligand and/or protein. RESULTS Tools are described for the analysis of ligand-protein contacts (LPC software) and contacts of structural units (CSU software) such as helices, sheets, strands and residues. Our approach is based on a detailed analysis of interatomic contacts and interface complementarity. For any ligand or structural unit, these software automatically: (i) calculate the solvent-accessible surface of every atom; (ii) determine the contacting residues and type of interaction they undergo (hydrophobic-hydrophobic, aromatic-aromatic, etc.); (iii) indicate all putative hydrogen bonds. LPC software further predicts changes in binding strength following chemical modification of the ligand. AVAILABILITY Both LPC and CSU can be accessed through the PDB and are integrated in the 3DB Atlas page of all PDB files. For any given file, the tools can also be accessed at http://www.pdb.bnl. gov/pdb-bin/lpc?PDB_ID= and http://www.pdb.bnl. gov/pdb-bin/csu?PDB_ID= with the four-letter PDB code added at the end in each case. Finally, LPC and CSU can be accessed at: http://sgedg.weizmann.ac.il/lpc and http://sgedg.weizmann.ac.il/csu.

Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submitted via PDBs WWW-based tool AutoDep, in either mmCIF or PDB format, and are most conveniently examined via PDBs WWW-based tool 3DB Browser.

PROTEIN DATA BANK ARCHIVES OF THREE-DIMENSIONAL MACROMOLECULAR STRUCTURES

Publisher Summary This chapter discusses the Protein Data Bank (PDB) archives of three-dimensional (3D) macromolecular structures. Several pieces of information related to an entry are archived by the PDB. In addition to the coordinate entry file, the PDB stores files related to the experiment such as structure factors, nuclear Overhauser effect (NOE) restraints, and lists of chemical shifts. Also archived are auxiliary files used in structure analysis and refinement such as X-PLOR parameter and topology files. Currently, the archives are managed as a set of individual files, and each entry may have several associated files. The PDB is in the process of building a relational database, 3Dbase that will replace the current data management and access system. A description of 3DBase, including an outline of the way users can access its contents is provided in the chapter. Coordinate entries in the PDB are stored in separate files, each of which reports the results of an experiment or analysis that elucidates the structure of proteins, nucleic acids, polysaccharides, and other biological macromolecules. Although most of the data are generated from single crystal X-ray diffraction studies, a growing number of PDB entries are from nuclear magnetic resonance (NMR) studies.

The Protein Data Bank: Current Status and Future Challenges

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of proteins, nucleic acids, and other biological macromolecules with a 25 year history of service to a global community. PDB is being replaced by 3DB, the Three-Dimensional Database of Biomolecular Structures that will continue to operate from Brookhaven National Laboratory. 3DB will be a highly sophisticated knowledge-based system for archiving and accessing structural information that combines the advantages of object oriented and relational database systems. 3DB will operate as a direct-deposition archive that will also accept third-party supplied annotations. Conversion of PDB to 3DB will be evolutionary, providing a high degree of compatibility with existing software.

The protein data bank. Bridging the gap between the sequence and 3D structure world.

The protein data bank (PDB), at Brookhaven National Laboratory, is a database containing information on experimentally determined three-dimensional structures of proteins, nucleic acids, and other biological macromolecules, with approximately 9000 entries. The PDB has a 27-year history of service to a global community of researchers, educators, and students in a wide variety of scientific disciplines. Data are easily submitted via PDBs WWW-based tool AutoDep, in either PDB or mmCIF format, and are most conveniently examined via PDBs WWW-based tool 3DB Browser. Collaborative centers have been, and continue to be, established worldwide to assist in data deposition, archiving, and distribution.

AutoDep: a web-based system for deposition and validation of macromolecular structural ­information

This paper describes the design and full implementation of a new concept in data deposition and validation: AutoDep (copyright Brookhaven Science Associates LLC). AutoDep changes the traditional procedure for data acceptance and validation of the primary databases into an interactive depositor-driven operation which almost eliminates the delay between the acceptance of the data and its public release. The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators for the complete and accurate description of the structural experiment and its results. AutoDep, developed by the Protein Data Bank at Brookhaven National Laboratory (BNL) as a flexible and portable system, has already been adopted by other primary databases and implemented on different platforms/operating systems. AutoDep was introduced at BNL in 1996 [see Manning (1996), Protein Data Bank Quart. Newslett. 77, 2 (ftp://ftp.rcsb. org/pub/pdb/doc/newsletters/bnl/newsletter96jul/newslttr+ ++.txt); Manning (1996), Protein Data Bank Quart. Newslett. 78, 2 (ftp://ftp. rcsb.org/pub/pdb/doc/newsletters/bnl/newsletter96oct/+ ++newslttr.txt)].

GETENTRY: a simple Unix script for accessing the Protein Data Bank's anonymous ftp server

The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/.