// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Volume 3. Number 1. February 1999. The NDB can be accessed through the BSR WWW site (http://ndbserver.rutgers.edu/) and its mirror sites (http://www.ebi.ac.uk/NDB/, http://ndbserver.nibh.go.jp/NDB/, http://ndb.sdsc.edu/). Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. ----------------------------------------------------------- Contents ----------------------------------------------------------- ADIT Validation Server Announcement Tsukuba Workshop on Nucleic Acid Structure and Interactions Proteins Plus Database moves to the PDB PDB News Data Curator Position Available for the RCSB PDB ----------------------------------------------------------- ADIT Validation Server (http://pdb.rutgers.edu/validate/) ----------------------------------------------------------- The Research Collaboratory for Structural Bioinformatics (RCSB), of which the NDB is a member, has released the ADIT Validation Server at http://pdb.rutgers.edu/validate/. ADIT (Auto Dep Input Tool) is the software used by the PDB for data processing of proteins and nucleic acid structures. As part of this process, the ADIT Validation Server checks the consistency of the coordinate format and performs a validation pre-check of structural features and structure factors. The ADIT Validation Server can be used independently of structure deposition and processing. In the future, the full functionality of ADIT will be made available and it will be used for structure deposition. The first step in using the ADIT Validation Server is running a Precheck of the coordinate format. The precheck will produce a brief report identifying any changes that need to be made in your data files in order to obtain a validation report. ADIT checks that the coordinate file is in either PDB or mmCIF format, includes a complete CRYST card (unit cell and space group information), and includes TER cards at the end of each chain and chain IDs. Scale cards must be provided if an alternate setting is being used for the space group symmetry. The second step is the creation of the validation report. The validation report includes an Atlas entry, a summary validation report, and a collection of structural diagnostics. Of particular interest to NDB users are the diagnostics from NUCheck (Zukang Feng, John Westbrook, and Helen M. Berman, 1998, Rutgers University, New Brunswick, NJ NDB-407). NUCheck is a program developed by the NDB that creates the following reports for the ADIT Validation Server: * Histogram reports for Bond Distance and Angle Comparisons: Sugar and phosphate bond lengths, Sugar and phosphate bond angles, Adenine bond distances, Adenine bond angles, Cytosine bond distances, Cytosine bond angles, Guanine bond distances, Guanine bond angles, Thymine bond distances, Thymine bond angles These histogram reports are generated by comparing values to the dictionaries described in: Anke Gelbin, Bohdan Schneider, Lester Clowney, Shu-Hsin Hsieh, Wilma K. Olson, and Helen M. Berman. (1996). Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents. J. Am. Chem. Soc., 118, 519-529. Lester Clowney, Shri C. Jain, A. R. Srinivasan, John Westbrook, Wilma K. Olson, and Helen M. Berman. (1996) Geometric Parameters in Nucleic Acids: Nitrogenous Bases. J. Am. Chem. Soc., 118, 509-518. * Scattergrams and Torsion Wheel Rings These reports refer to the conformational preferences described in: Bohdan Schneider, Stephen Neidle and Helen M. Berman. (1997). Conformations of the Sugar-Phosphate Backbone in Helical DNA Crystal Structures. Biopoly., 42, 113-124. * Base Morphology Comparison Histograms These reports are generated from using CURVES V5.1: R. Lavery and H. Sklenar (1988). The Definition of Generalised Helicoidal Parameters and of Axis Curvature in Irregular Nucleic Acids. Biomol. Struct. Dynam., 6, 63-91. * Molecular graphics of the asymmetric unit and crystal packing are available in GIF and VRML formats from the Atlas page. Proteins and protein-nucleic acid structures can also be validated using ADIT. The ADIT validation server provides reports from PROCHECK (R.A. Laskowski, M.W. MacArthur, D.S. Moss and J.M. Thornton. (1993). J. Appl. Cryst., 26, 283-291.) and SFCHECK (A.A. Vaguine, J. Richelle, and S.J. Wodak. (1999). Acta Cryst. D55, 191-205). Tutorials for using the ADIT Validation Server are available online. Questions can be sent to deposit@rcsb.rutgers.edu. Tsukuba Workshop on Nucleic Acid Structure and Interactions ----------------------------------------------------------- The Tsukuba Workshop on Nucleic Acid Structure and Interactions was held at the Structural Biology Centre in Tsukuba, Japan on January 12-14, 1999. The meeting was funded by the COE program of Science and Technology Agency, Japan, and the CREST program of Japan Science and Technology corporation. The meeting was organized by Masashi Suzuki of the National Institute of Bioscience and Human-Technology and Helen M. Berman and Wilma Olson of the Nucleic Acid Database Project. Topics discussed included the finalization of the parameters used to describe nucleic acid structure, ways to describe global features of nucleic acid structure, how best to describe the interface between nucleic acids and proteins, and ways to describe RNA structure. The proceedings of this workshop should appear in a future journal article. Proteins Plus Database moves to the PDB ----------------------------------------------------------- The Proteins Plus Database, which was part of Structure Finder, is now the core database for the new Protein Data Bank (PDB) under the management of the RCSB. As a result, the structure finder interface and the proteins-plus directory on the NDB FTP server will be removed. These resources are now merged with the resources at http://www.rcsb.org/. The other Structure Finder databases (Nucleic Acid-NMR, DNA-Binding Proteins, and the NDB) and their FTP directories will continue to be available at http://ndbserver.rutgers.edu/. PDB News ----------------------------------------------------------- The RCSB has made several new developments at the PDB, which are described in detail in the first RCSB PDB newsletter (http://www.rcsb.org/pdb/newsletter/). These developments include: * Protein crystal structures and NMR data deposited at the PDB on or after January 27, 1999 will be processed and released by the RCSB at all PDB sites. Nucleic acid crystal structures will continue to be processed by the NDB. * A new query tool developed by the RCSB, called PDB SearchLite, is now available. * The PDB FTP site, in the same structure and format, is available from the RCSB, its mirror sites and the BNL PDB web sites. Full descriptions of these developments and the latest RCSB news are available at http://www.rcsb.org/. Data Curator Position Available for the RCSB PDB ------------------------------------------------------------ The management of the Protein Data Bank (PDB) has moved from Brookhaven to the Research Collaboratory for Structural Bioinformatics at Rutgers University, UCSD, and NIST. A position is available at Rutgers University for a person to curate and standardize the representation of macromolecular structures for the PDB. Experience in structural biology and a working knowledge of UNIX is required. The successful candidate must be able to pay close attention to detail and meet stringent deadlines. This position offers the opportunity to participate in an exciting project with significant impact on the scientific community. Please send a cover letter and curriculum vitae to Dr. Helen M. Berman, Rutgers, The State University of New Jersey, Department of Chemistry, 610 Taylor Rd, Piscataway, NJ 08854-8087. e-mail: pdbadmin@rcsb.rutgers.edu, Phone: (732) 445-0103, Fax: (732) 445-4320. ----------------------------------------------------------- NDB Staff: Helen M. Berman, Director Zukang Feng, Shri Jain, Bohdan Schneider, John Westbrook, and Christine Zardecki The Nucleic Acid Database Project is funded by the National Science Foundation and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //