Protein structure resources.

The Protein Data Bank (PDB) is the primary source of macromolecular structure data for a worldwide community of users. A subset of those users then process these data to derive secondary information which is also available on the WWW. This process includes validation, some form of reductionism, via sequence or structure, or visualization. The result, a set of further web-accessible resources on protein structure and functional classification, links to primary genomic information, protein-protein and protein-ligand interactions, protein dynamics and protein-modeling resources. This paper reports on these processes and a subset of the web resources that result.

[1]  M. L. Jones,et al.  PDBsum: a Web-based database of summaries and analyses of all PDB structures. , 1997, Trends in biochemical sciences.

[2]  M. Gerstein,et al.  The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. , 2000, Nucleic acids research.

[3]  Patrice Koehl,et al.  The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..

[4]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[5]  P E Bourne,et al.  An alternative view of protein fold space , 2000, Proteins.

[6]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[7]  A. Sali,et al.  Structural genomics: beyond the Human Genome Project , 1999, Nature Genetics.

[8]  John E. Johnson,et al.  Virus Particle Explorer (VIPER), a Website for Virus Capsid Structures and Their Computational Analyses , 2001, Journal of Virology.

[9]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[10]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[11]  E. Koonin,et al.  The Impact of Comparative Genomics on Our Understanding of Evolution , 2000, Cell.

[12]  H M Berman,et al.  Protein-DNA interactions: A structural analysis. , 1999, Journal of molecular biology.

[13]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[14]  P E Bourne,et al.  The protein kinase resource. , 1997, Trends in biochemical sciences.

[15]  W G Krebs,et al.  PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. , 2001, Nucleic acids research.

[16]  A. Lesk,et al.  How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.

[17]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[18]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[19]  Jan Reichert,et al.  The IMB Jena Image Library of Biological Macromolecules: 2002 update , 2002, Nucleic Acids Res..

[20]  J. Thornton,et al.  Stereochemical quality of protein structure coordinates , 1992, Proteins.

[21]  E V Koonin,et al.  Estimating the number of protein folds and families from complete genome data. , 2000, Journal of molecular biology.

[22]  C Sander,et al.  Mapping the Protein Universe , 1996, Science.

[23]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[24]  Jürg Nievergelt,et al.  Emerging concepts in computer graphics , 1970 .

[25]  Philip E. Bourne,et al.  An analysis of the Protein Data Bank in search of temporal and global trends , 1999, Bioinform..

[26]  J S Richardson,et al.  Schematic drawings of protein structures. , 1985, Methods in enzymology.