Literature DB >> 15840705

HCPM--program for hierarchical clustering of protein models.

Dominik Gront1, Andrzej Kolinski.   

Abstract

HCPM is a tool for clustering protein structures from comparative modeling, ab initio structure prediction, etc. A hierarchical clustering algorithm is designed and tested, and a heuristic is provided for an optimal cluster selection. The method has been successfully tested during the CASP6 experiment.

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Year:  2005        PMID： 15840705     DOI： 10.1093/bioinformatics/bti450

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  11 in total

1.  Folding pathway of the b1 domain of protein G explored by multiscale modeling.

Authors:  Sebastian Kmiecik; Andrzej Kolinski
Journal:  Biophys J       Date:  2007-09-21       Impact factor: 4.033

2.  Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

Authors:  Taner Z Sen; Margaret Kloster; Robert L Jernigan; Andrzej Kolinski; Janusz M Bujnicki; Andrzej Kloczkowski
Journal:  Biophys J       Date:  2008-01-04       Impact factor: 4.033

3.  Elastic network normal modes provide a basis for protein structure refinement.

Authors:  Pawel Gniewek; Andrzej Kolinski; Robert L Jernigan; Andrzej Kloczkowski
Journal:  J Chem Phys       Date:  2012-05-21       Impact factor: 3.488

4.  Network mapping of the conformational heterogeneity of SOD1 by deploying statistical cluster analysis of FTIR spectra.

Authors:  Sourav Chowdhury; Sagnik Sen; Amrita Banerjee; Vladimir N Uversky; Ujjwal Maulik; Krishnananda Chattopadhyay
Journal:  Cell Mol Life Sci       Date:  2019-04-22       Impact factor: 9.261

5.  Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid.

Authors:  Mateusz Kurcinski; Andrzej Kolinski
Journal:  J Steroid Biochem Mol Biol       Date:  2010-04-14       Impact factor: 4.292

6.  Hierarchical modeling of protein interactions.

Authors:  Mateusz Kurcinski; Andrzej Kolinski
Journal:  J Mol Model       Date:  2007-02-13       Impact factor: 1.810

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

Authors:  Jianjun Zhou; David S Wishart
Journal:  BMC Bioinformatics       Date:  2013-01-16       Impact factor: 3.169

8.  Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained models.

Authors:  Dorota Latek; Andrzej Kolinski
Journal:  BMC Struct Biol       Date:  2008-08-11

9.  Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.

Authors:  Elena M Ibryashkina; Marina V Zakharova; Vladimir B Baskunov; Ekaterina S Bogdanova; Maxim O Nagornykh; Marat M Den'mukhamedov; Bogdan S Melnik; Andrzej Kolinski; Dominik Gront; Marcin Feder; Alexander S Solonin; Janusz M Bujnicki
Journal:  BMC Struct Biol       Date:  2007-07-12

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

Authors:  Sebastian Kmiecik; Dominik Gront; Andrzej Kolinski
Journal:  BMC Struct Biol       Date:  2007-06-29
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