Literature DB >> 8019422

Enlarged representative set of protein structures.

U Hobohm1, C Sander.   

Abstract

To reduce redundancy in the Protein Data Bank of 3D protein structures, which is caused by many homologous proteins in the data bank, we have selected a representative set of structures. The selection algorithm was designed to (1) select as many nonhomologous structures as possible, and (2) to select structures of good quality. The representative set may reduce time and effort in statistical analyses.

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Year:  1994        PMID: 8019422      PMCID: PMC2142698          DOI: 10.1002/pro.5560030317

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  5 in total

1.  Selection of representative protein data sets.

Authors:  U Hobohm; M Scharf; R Schneider; C Sander
Journal:  Protein Sci       Date:  1992-03       Impact factor: 6.725

2.  A database of protein structure families with common folding motifs.

Authors:  L Holm; C Ouzounis; C Sander; G Tuparev; G Vriend
Journal:  Protein Sci       Date:  1992-12       Impact factor: 6.725

3.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

4.  Prediction of protein secondary structure at better than 70% accuracy.

Authors:  B Rost; C Sander
Journal:  J Mol Biol       Date:  1993-07-20       Impact factor: 5.469

5.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

  5 in total
  185 in total

1.  Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements.

Authors:  K Kinoshita; A Kidera; N Go
Journal:  Protein Sci       Date:  1999-06       Impact factor: 6.725

2.  Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments.

Authors:  I Friedberg; T Kaplan; H Margalit
Journal:  Protein Sci       Date:  2000-11       Impact factor: 6.725

3.  PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).

Authors:  T Noguchi; H Matsuda; Y Akiyama
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  Identification of related proteins with weak sequence identity using secondary structure information.

Authors:  C Geourjon; C Combet; C Blanchet; G Deléage
Journal:  Protein Sci       Date:  2001-04       Impact factor: 6.725

5.  Comparative conformational analysis of peptide libraries.

Authors:  S G Jacchieri
Journal:  Mol Divers       Date:  1998       Impact factor: 2.943

6.  A statistical mechanical method to optimize energy functions for protein folding.

Authors:  U Bastolla; M Vendruscolo; E W Knapp
Journal:  Proc Natl Acad Sci U S A       Date:  2000-04-11       Impact factor: 11.205

7.  Novel disulfide engineering in human carbonic anhydrase II using the PAIRWISE side-chain geometry database.

Authors:  R E Burton; J A Hunt; C A Fierke; T G Oas
Journal:  Protein Sci       Date:  2000-04       Impact factor: 6.725

8.  Measures of residue density in protein structures.

Authors:  F Baud; S Karlin
Journal:  Proc Natl Acad Sci U S A       Date:  1999-10-26       Impact factor: 11.205

9.  A survey of left-handed polyproline II helices.

Authors:  B J Stapley; T P Creamer
Journal:  Protein Sci       Date:  1999-03       Impact factor: 6.725

10.  The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding.

Authors:  R V Pappu; R Srinivasan; G D Rose
Journal:  Proc Natl Acad Sci U S A       Date:  2000-11-07       Impact factor: 11.205

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