Literature DB >> 15996119

New assessment of a structural alphabet.

Alexandre G de Brevern1.   

Abstract

A statistical analysis of the Protein Databank (PDB) structures had led us to define a set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one defined by the (phi, psi) dihedral angles of 5 consecutive residues. Here, we analyze the effect of the enlargement of the PDB on the PBs' definition. The results highlight the quality of the 3D approximation ensured by the PBs. These last could be of great interest in ab initio modeling.

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Year:  2005        PMID： 15996119      PMCID： PMC2001288     

Source DB:  PubMed          Journal:  In Silico Biol        ISSN： 1386-6338


  21 in total

1.  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

2.  HELANAL: a program to characterize helix geometry in proteins.

Authors:  M Bansal; S Kumar; R Velavan
Journal:  J Biomol Struct Dyn       Date:  2000-04

3.  Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks.

Authors:  A G de Brevern; C Etchebest; S Hazout
Journal:  Proteins       Date:  2000-11-15

4.  'Hybrid protein model' for optimally defining 3D protein structure fragments.

Authors:  A G de Brevern; S Hazout
Journal:  Bioinformatics       Date:  2003-02-12       Impact factor: 6.937

5.  Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.

Authors:  Rachel Karchin; Melissa Cline; Yael Mandel-Gutfreund; Kevin Karplus
Journal:  Proteins       Date:  2003-06-01

6.  Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.

Authors:  Alexandre G de Brevern; Hélène Valadié; Serge Hazout; Catherine Etchebest
Journal:  Protein Sci       Date:  2002-12       Impact factor: 6.725

7.  Conformational subspace in simulation of early-stage protein folding.

Authors:  Wiktor Jurkowski; Michał Brylinski; Leszek Konieczny; Zdzisław Wiíniowski; Irena Roterman
Journal:  Proteins       Date:  2004-04-01

8.  Loops In Proteins (LIP)--a comprehensive loop database for homology modelling.

Authors:  E Michalsky; A Goede; R Preissner
Journal:  Protein Eng       Date:  2003-12

9.  Local backbone structure prediction of proteins.

Authors:  Alexandre G de Brevern; Cristina Benros; Romain Gautier; Héléne Valadié; Serge Hazout; Catherine Etchebest
Journal:  In Silico Biol       Date:  2004

10.  A structural alphabet for local protein structures: improved prediction methods.

Authors:  Catherine Etchebest; Cristina Benros; Serge Hazout; Alexandre G de Brevern
Journal:  Proteins       Date:  2005-06-01
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  27 in total

1.  Cis-trans peptide variations in structurally similar proteins.

Authors:  Agnel Praveen Joseph; Narayanaswamy Srinivasan; Alexandre G de Brevern
Journal:  Amino Acids       Date:  2012-01-08       Impact factor: 3.520

2.  Prediction of ketoacyl synthase family using reduced amino acid alphabets.

Authors:  Wei Chen; Pengmian Feng; Hao Lin
Journal:  J Ind Microbiol Biotechnol       Date:  2011-10-26       Impact factor: 3.346

3.  "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence.

Authors:  A G De Brevern; C Etchebest; C Benros; S Hazout
Journal:  J Biosci       Date:  2007-01       Impact factor: 1.826

4.  A new prediction strategy for long local protein structures using an original description.

Authors:  Aurélie Bornot; Catherine Etchebest; Alexandre G de Brevern
Journal:  Proteins       Date:  2009-08-15

5.  β-Bulges: extensive structural analyses of β-sheets irregularities.

Authors:  Pierrick Craveur; Agnel Praveen Joseph; Joseph Rebehmed; Alexandre G de Brevern
Journal:  Protein Sci       Date:  2013-09-14       Impact factor: 6.725

6.  Analysis of loop boundaries using different local structure assignment methods.

Authors:  Manoj Tyagi; Aurélie Bornot; Bernard Offmann; Alexandre G de Brevern
Journal:  Protein Sci       Date:  2009-09       Impact factor: 6.725

Review 7.  In silico studies on DARC.

Authors:  Alexandre G de Brevern; Ludovic Autin; Yves Colin; Olivier Bertrand; Catherine Etchebest
Journal:  Infect Disord Drug Targets       Date:  2009-06

8.  New opportunities to fight against infectious diseases and to identify pertinent drug targets with novel methodologies.

Authors:  Alexandre G de Brevern
Journal:  Infect Disord Drug Targets       Date:  2009-06

9.  A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.

Authors:  C Etchebest; C Benros; A Bornot; A-C Camproux; A G de Brevern
Journal:  Eur Biophys J       Date:  2007-06-13       Impact factor: 1.733

10.  A short survey on protein blocks.

Authors:  Agnel Praveen Joseph; Garima Agarwal; Swapnil Mahajan; Jean-Christophe Gelly; Lakshmipuram S Swapna; Bernard Offmann; Frédéric Cadet; Aurélie Bornot; Manoj Tyagi; Hélène Valadié; Bohdan Schneider; Catherine Etchebest; Narayanaswamy Srinivasan; Alexandre G De Brevern
Journal:  Biophys Rev       Date:  2010-08-05
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