Literature DB >> 16479277

Exploring protein energy landscapes with hierarchical clustering.

Dominik Gront, Ulrich H E Hansmann, Andrzej Kolinski.   

Abstract

In this work we present a new method for investigating local energy minima on a protein energy landscape. The CABS (CAlpha, CBeta and the center of mass of the Side chain) method was employed for generating protein models, but any other method could be used instead. Cα traces from an ensemble of models are hierarchical clustered with the HCPM (Hierarchical Clustering of Protein Models) method. The efficiency of this method for sampling and analyzing energy landscapes is shown.

Year:  2005        PMID： 16479277      PMCID： PMC1366497          DOI： 10.1002/qua.20741

Source DB:  PubMed          Journal:  Int J Quantum Chem        ISSN： 0020-7608            Impact factor:   2.444


  6 in total

Review 1.  Protein modeling and structure prediction with a reduced representation.

Authors:  Andrzej Kolinski
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2.  An improved protein decoy set for testing energy functions for protein structure prediction.

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3.  Clustering of low-energy conformations near the native structures of small proteins.

Authors:  D Shortle; K T Simons; D Baker
Journal:  Proc Natl Acad Sci U S A       Date:  1998-09-15       Impact factor: 11.205

4.  Energy functions that discriminate X-ray and near native folds from well-constructed decoys.

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Journal:  J Mol Biol       Date:  1996-05-03       Impact factor: 5.469

Review 5.  Principles of protein folding--a perspective from simple exact models.

Authors:  K A Dill; S Bromberg; K Yue; K M Fiebig; D P Yee; P D Thomas; H S Chan
Journal:  Protein Sci       Date:  1995-04       Impact factor: 6.725

6.  Recognition of errors in three-dimensional structures of proteins.

Authors:  M J Sippl
Journal:  Proteins       Date:  1993-12
  6 in total
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Journal:  J Phys Chem B       Date:  2007-01-11       Impact factor: 2.991

Review 2.  Understanding protein folding: small proteins in silico.

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4.  A multilayer evaluation approach for protein structure prediction and model quality assessment.

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5.  NEW MDS AND CLUSTERING BASED ALGORITHMS FOR PROTEIN MODEL QUALITY ASSESSMENT AND SELECTION.

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Journal:  Int J Artif Intell Tools       Date:  2013-10-25       Impact factor: 1.208

6.  An improved method to detect correct protein folds using partial clustering.

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Journal:  BMC Bioinformatics       Date:  2013-01-16       Impact factor: 3.169

7.  Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field.

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8.  BioShell 3.0: Library for Processing Structural Biology Data.

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9.  Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.

Authors:  Adam Liwo; Cezary Czaplewski; Adam K Sieradzan; Agnieszka G Lipska; Sergey A Samsonov; Rajesh K Murarka
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  9 in total

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