Literature DB >> 10739263

Expectations from structural genomics.

S E Brenner1, M Levitt.   

Abstract

Structural genomics projects aim to provide an experimental structure or a good model for every protein in all completed genomes. Most of the experimental work for these projects will be directed toward proteins whose fold cannot be readily recognized by simple sequence comparison with proteins of known structure. Based on the history of proteins classified in the SCOP structure database, we expect that only about a quarter of the early structural genomics targets will have a new fold. Among the remaining ones, about half are likely to be evolutionarily related to proteins of known structure, even though the homology could not be readily detected by sequence analysis.

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Year:  2000        PMID: 10739263      PMCID: PMC2144435          DOI: 10.1110/ps.9.1.197

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


  16 in total

1.  Estimating the total number of protein folds.

Authors:  S Govindarajan; R Recabarren; R A Goldstein
Journal:  Proteins       Date:  1999-06-01

2.  Protein folds and functions.

Authors:  A C Martin; C A Orengo; E G Hutchinson; S Jones; M Karmirantzou; R A Laskowski; J B Mitchell; C Taroni; J M Thornton
Journal:  Structure       Date:  1998-07-15       Impact factor: 5.006

Review 3.  Shining a light on structural genomics.

Authors:  S H Kim
Journal:  Nat Struct Biol       Date:  1998-08

Review 4.  Mapping the protein universe.

Authors:  L Holm; C Sander
Journal:  Science       Date:  1996-08-02       Impact factor: 47.728

5.  Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.

Authors:  S E Brenner; C Chothia; T J Hubbard
Journal:  Proc Natl Acad Sci U S A       Date:  1998-05-26       Impact factor: 11.205

Review 6.  Population statistics of protein structures: lessons from structural classifications.

Authors:  S E Brenner; C Chothia; T J Hubbard
Journal:  Curr Opin Struct Biol       Date:  1997-06       Impact factor: 6.809

7.  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

Review 8.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

9.  SCOP: a structural classification of proteins database for the investigation of sequences and structures.

Authors:  A G Murzin; S E Brenner; T Hubbard; C Chothia
Journal:  J Mol Biol       Date:  1995-04-07       Impact factor: 5.469

10.  Protein superfamilies and domain superfolds.

Authors:  C A Orengo; D T Jones; J M Thornton
Journal:  Nature       Date:  1994-12-15       Impact factor: 49.962

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  33 in total

1.  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

2.  CKAAPs DB: a conserved key amino acid positions database.

Authors:  W W Li; B V Reddy; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  Estimating the probability for a protein to have a new fold: A statistical computational model.

Authors:  E Portugaly; M Linial
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-09       Impact factor: 11.205

4.  Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function.

Authors:  Iddo Friedberg; Hanah Margalit
Journal:  Protein Sci       Date:  2002-02       Impact factor: 6.725

5.  MODBASE, a database of annotated comparative protein structure models.

Authors:  Ursula Pieper; Narayanan Eswar; Ashley C Stuart; Valentin A Ilyin; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.

Authors:  Shashi B Pandit; Dilip Gosar; S Abhiman; S Sujatha; Sayali S Dixit; Natasha S Mhatre; R Sowdhamini; N Srinivasan
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome.

Authors:  Franca Fraternali; Luigi Cavallo
Journal:  Nucleic Acids Res       Date:  2002-07-01       Impact factor: 16.971

8.  MODBASE, a database of annotated comparative protein structure models, and associated resources.

Authors:  Ursula Pieper; Narayanan Eswar; Hannes Braberg; M S Madhusudhan; Fred P Davis; Ashley C Stuart; Nebojsa Mirkovic; Andrea Rossi; Marc A Marti-Renom; Andras Fiser; Ben Webb; Daniel Greenblatt; Conrad C Huang; Thomas E Ferrin; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  Role for NMR in structural genomics.

Authors:  Michael A Kennedy; Gaetano T Montelione; Cheryl H Arrowsmith; John L Markley
Journal:  J Struct Funct Genomics       Date:  2002

10.  ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence.

Authors:  J L Klepeis; C A Floudas
Journal:  Biophys J       Date:  2003-10       Impact factor: 4.033

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