Literature DB >> 9872054

Contemporary approaches to protein structure classification.

M B Swindells1, C A Orengo, D T Jones, E G Hutchinson, J M Thornton.   

Abstract

In a similar manner to sequence database searching, it is also possible to compare three-dimensional protein structure. Such methods can be extremely useful because a structural similarity may represent a distant evolutionary relationship that is undetectable by sequence analysis. In this review, we summarise the most popular structure comparison methods, show how they can be used for database searching, and then describe some of the most advanced attempts to develop comprehensive protein structure classifications. With such data, it is possible to identify distant evolutionary relationships, provide libraries of unique folds for structure prediction, estimate the total number of folds that exist, and investigate the preference for certain types of structures over others.

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Year:  1998        PMID： 9872054     DOI： 10.1002/(SICI)1521-1878(199811)20:11<884::AID-BIES3>3.0.CO;2-H

Source DB:  PubMed          Journal:  Bioessays        ISSN： 0265-9247            Impact factor:   4.345


  16 in total

1.  Automated diagnosis of data-model conflicts using metadata.

Authors:  R O Chen; R B Altman
Journal:  J Am Med Inform Assoc       Date:  1999 Sep-Oct       Impact factor: 4.497

2.  Plasticity of quaternary structure: twenty-two ways to form a LacI dimer.

Authors:  L Swint-Kruse; C R Elam; J W Lin; D R Wycuff; K Shive Matthews
Journal:  Protein Sci       Date:  2001-02       Impact factor: 6.725

3.  An evolutionarily structured universe of protein architecture.

Authors:  Gustavo Caetano-Anollés; Derek Caetano-Anollés
Journal:  Genome Res       Date:  2003-07       Impact factor: 9.043

Review 4.  Structural genomics: computational methods for structure analysis.

Authors:  Sharon Goldsmith-Fischman; Barry Honig
Journal:  Protein Sci       Date:  2003-09       Impact factor: 6.725

5.  Mapping protein pockets through their potential small-molecule binding volumes: QSCD applied to biological protein structures.

Authors:  Keith Mason; Nehal M Patel; Aric Ledel; Ciamac C Moallemi; Edward A Wintner
Journal:  J Comput Aided Mol Des       Date:  2004-01       Impact factor: 3.686

6.  Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily.

Authors:  Kaitlyn M Guardino; Sarah R Sheftic; Robert E Slattery; Andrei T Alexandrescu
Journal:  Int J Mol Sci       Date:  2009-05-22       Impact factor: 6.208

7.  Automatic structure classification of small proteins using random forest.

Authors:  Pooja Jain; Jonathan D Hirst
Journal:  BMC Bioinformatics       Date:  2010-07-01       Impact factor: 3.169

8.  The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network.

Authors:  Rosa Tarrío; Francisco J Ayala; Francisco Rodríguez-Trelles
Journal:  PLoS One       Date:  2011-07-26       Impact factor: 3.240

9.  Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.

Authors:  Garima Agarwal; Swapnil Mahajan; Narayanaswamy Srinivasan; Alexandre G de Brevern
Journal:  PLoS One       Date:  2011-03-18       Impact factor: 3.240

Review 10.  Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds.

Authors:  Nicola Bordin; Ian Sillitoe; Jonathan G Lees; Christine Orengo
Journal:  Front Mol Biosci       Date:  2021-05-10
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