Literature DB >> 9232660

Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns.

K F Han1, C Bystroff, D Baker.   

Abstract

We have used cluster analysis to identify recurring sequence patterns that transcend protein family boundaries. A subset of these patterns occur predominantly in a single type of local structure in proteins. Here we characterize the three-dimensional structures and contexts in which these sequence patterns occur, with particular attention to the interactions responsible for their structural selectivity.

Mesh：

Year:  1997        PMID： 9232660      PMCID： PMC2143736          DOI： 10.1002/pro.5560060723

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


  12 in total

1.  A method to identify protein sequences that fold into a known three-dimensional structure.

Authors:  J U Bowie; R Lüthy; D Eisenberg
Journal:  Science       Date:  1991-07-12       Impact factor: 47.728

2.  Recurring local sequence motifs in proteins.

Authors:  K F Han; D Baker
Journal:  J Mol Biol       Date:  1995-08-04       Impact factor: 5.469

Review 3.  Local sequence-structure correlations in proteins.

Authors:  C Bystroff; K T Simons; K F Han; D Baker
Journal:  Curr Opin Biotechnol       Date:  1996-08       Impact factor: 9.740

4.  Global properties of the mapping between local amino acid sequence and local structure in proteins.

Authors:  K F Han; D Baker
Journal:  Proc Natl Acad Sci U S A       Date:  1996-06-11       Impact factor: 11.205

Review 5.  Empirical predictions of protein conformation.

Authors:  P Y Chou; G D Fasman
Journal:  Annu Rev Biochem       Date:  1978       Impact factor: 23.643

6.  LINUS: a hierarchic procedure to predict the fold of a protein.

Authors:  R Srinivasan; G D Rose
Journal:  Proteins       Date:  1995-06

7.  Bona fide prediction of aspects of protein conformation. Assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences.

Authors:  S A Benner; I Badcoe; M A Cohen; D L Gerloff
Journal:  J Mol Biol       Date:  1994-01-21       Impact factor: 5.469

8.  Determination of the conformation of folding initiation sites in proteins by computer simulation.

Authors:  F Avbelj; J Moult
Journal:  Proteins       Date:  1995-10

9.  Helix stop signals in proteins and peptides: the capping box.

Authors:  E T Harper; G D Rose
Journal:  Biochemistry       Date:  1993-08-03       Impact factor: 3.162

10.  Rules for alpha-helix termination by glycine.

Authors:  R Aurora; R Srinivasan; G D Rose
Journal:  Science       Date:  1994-05-20       Impact factor: 47.728
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  6 in total

1.  Some fundamental aspects of building protein structures from fragment libraries.

Authors:  J Bradley Holmes; Jerry Tsai
Journal:  Protein Sci       Date:  2004-06       Impact factor: 6.725

2.  From residue coevolution to protein conformational ensembles and functional dynamics.

Authors:  Ludovico Sutto; Simone Marsili; Alfonso Valencia; Francesco Luigi Gervasio
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-20       Impact factor: 11.205

3.  Fragment-HMM: a new approach to protein structure prediction.

Authors:  Shuai Cheng Li; Dongbo Bu; Jinbo Xu; Ming Li
Journal:  Protein Sci       Date:  2008-08-22       Impact factor: 6.725

4.  Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins.

Authors:  Annalisa Marsico; Andreas Henschel; Christof Winter; Anne Tuukkanen; Boris Vassilev; Kerstin Scheubert; Michael Schroeder
Journal:  BMC Bioinformatics       Date:  2010-04-26       Impact factor: 3.169

5.  Local protein structure prediction using discriminative models.

Authors:  Oliver Sander; Ingolf Sommer; Thomas Lengauer
Journal:  BMC Bioinformatics       Date:  2006-01-11       Impact factor: 3.169

6.  Recurrent structural motifs in non-homologous protein structures.

Authors:  Maria U Johansson; Vincent Zoete; Nicolas Guex
Journal:  Int J Mol Sci       Date:  2013-04-10       Impact factor: 5.923
  6 in total

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