San Diego Supercomputer Center

The authors gratefully acknowledge the support of the U.S. Department of Agriculture (Award 94-37303), the National Science Foundation (Award MCB94-08999) and the San Diego Supercomputer Center. 

PDB is one of the oldest protein data bases, founded in 1971. It has three locations, Rutgers University in New Jersey, San Diego Supercomputer Center (SDSC) at the University of California, and the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. The PDB is a source for protein characterization and structure as well. The PDB archive contains macromolecular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses. Approximately 50-100 new structures are deposited each week, which are annotated and released upon the depositor s specifications. PDB data are freely available worldwide. PDB formats, annotates, validates, and releases dozens of complicated structure files each week some of them take only a couple of hours, others take weeks to process. Data processing is the main task of people at the PDB and validation is the most time-consuming part (Smith-Schmidt, 2002). 

I thank M. Nio, J. Zollweg, R. Sinkovits, R. Leary, T. Tannenbaum, and J. Ballard for assistance in various phases of computation. The bulk of computation has been carried out on the IBM SP2 and SP3 computers at San Diego Supercomputer Center, IBM SP2 at the Center for Parallel Computing (University of Michigan), and the Condor system at the University of Wisconsin, which are made available by the computing award of the National Resource Allocation Committee. Some part of work has been carried out on the IBM SP2 at Cornell Theory Center. This work is supported in part by the U. S. National Science Foundation. 

San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive 0505, La Jolla, CA 92093-0505, USA... 

In addition to ab initio methods, developments for semiempirical methods are being investigated on parallel machines. Notable in this regard are MOPAC > 20 (at the San Diego Supercomputer Center i EPSRC Dares-bury Laboratory ) and AMSOL.122 expected, many of the problems encountered with ab initio codes are also found with these programs. 

This work was supported by the National Science Foundation. BJS thanks Dave Vanden Bout for many stimulating discussions. BJS gratehilly acknowledges the support of a National Science Foundation Postdoctoral Fellowship in Chemistry, and the allocation of computational resources from the San Diego Supercomputing Center. 

The Protein Data Bank (PDB) (27, 28) is now coordinated by a consortium of several institutions (Rutgers University, the San Diego Supercomputer Center, and National Institute for Standards and Technology). As of this writing, the PDB has over 18,000 structures. 

Acknowledgment. Part of this research has been supported by the San Diego Supercomputer Center. 

We thank the National Science Foundation (grant no. CTS-9896195) for their support of this work and for the Mctacentcr grant (no. MCA93S01 IP) and NRAC allocation (no. MCA93S011) which made these calculations possible, and the staffs of the Cornell Theory Center and the San Diego Supercomputer Center for their general assistance. 

The authors acknowledge support from the Howard Hughes Medical Institute, the National Institutes of Health, the National Science Foundation, the Keck Foundation, the National Biomedical Computing Resource, the San Diego Supercomputer Center, and Accelrys, Inc. 

International Society for Computational Biology c/o the San Diego Supercomputer Center. UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, U.S.A. Phone +1 858-822-0852, Fax +1 760-522-8805. E-mail admin iscb.org. URL http //www.iscb.org/. Emphasis is on the role of computing and informatics in advancing molecular biology. 

The CMS Molecular Biology Resource [168] at the San Diego Supercomputer Center contains an excellent compendium of Web-accessible bioinformatics tools. The ExPASy (Expert Protein Analysis System] proteomics server of the Swiss Institute of Bioinformatics [169] and the EBI Toolbox are two other popular tool collections. Another useful resource is Herbert Mayer s Bioinformatics World Web site, which contains a comprehensive collection of bioinformatics tools and software, including evaluations, comments, and tutorials. 

Momany, F.A., Klimkowski.VJ., Pitha, R. and Venkatachalam, C.M., "Molecular Design using Supercomputers", Video Presentation, San Diego State University and San Diego Supercomputer Center, April 20,... 

This work was supported at the University of South Alabama in part by the donors of the Petroleum Research Fund, administered by the American Chemical Society, Cray Research, and IBM Corporation, and at the University of Houston by the Robert A. Welch Foundation, the National Institutes of Health (NIH), the National Center for Supercomputing Applications, and the San Diego Supercomputer Center. MKG is the recipient of the Howard Hughes Postdoctoral Fellowship for Physicians, and BAL is the recipient of an NIH predoctoral traineeship in the Houston Area Molecular Biophysics Training Program. 

The Protein Kinase Resource Center. San Diego Supercomputer Center. Available from . 

San Diego Supercomputer Center University of California at San Diego,... 

Cornell Theory Center National Center for Atmospheric Research National Center for Supercomputing Applications Ohio Supercomputer Center Pittsburgh Supercomputing Center San Diego Supercomputer Center 607-254-8610 303-497-1225 217-244-0072 614-292-9248 412-268-6350 619-534-5000 consult ctc.edu scdinfo ncar.ucar.edu consult ncsa.uiuc.edu osdnfo oscedu remarks psc.edu consult sdsc.edu... 

PETER R. TAYLOR San Diego Supercomputer Center P. 0. Box 85608, San Diego CA 92186-9784 USA... 

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