Literature DB >> 15093839

Voronoi and Voronoi-related tessellations in studies of protein structure and interaction.

Anne Poupon1.   

Abstract

The three-dimensional structure of a protein can be modeled by a set of polyhedra drawn around its atoms or residues. The tessellation invented by Voronoi in 1908, and other tessellations of space derived from it, provide versatile representations of three-dimensional structures. In recent years, they have been used to investigate a series of issues relating to proteins: atom and residue volumes, packing, folding, interactions and binding.

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Year:  2004        PMID: 15093839     DOI: 10.1016/j.sbi.2004.03.010

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  26 in total

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Journal:  Nat Nanotechnol       Date:  2012-07-08       Impact factor: 39.213

2.  Revisiting the Voronoi description of protein-protein interfaces.

Authors:  Frédéric Cazals; Flavien Proust; Ranjit P Bahadur; Joël Janin
Journal:  Protein Sci       Date:  2006-09       Impact factor: 6.725

3.  Predicting protein folding rates from geometric contact and amino acid sequence.

Authors:  Zheng Ouyang; Jie Liang
Journal:  Protein Sci       Date:  2008-04-23       Impact factor: 6.725

Review 4.  Decoding HIV resistance: from genotype to therapy.

Authors:  Irene T Weber; Robert W Harrison
Journal:  Future Med Chem       Date:  2017-08-09       Impact factor: 3.808

5.  An amino acid packing code for α-helical structure and protein design.

Authors:  Hyun Joo; Archana G Chavan; Jamie Phan; Ryan Day; Jerry Tsai
Journal:  J Mol Biol       Date:  2012-03-15       Impact factor: 5.469

6.  Characterization of 3D Voronoi tessellation nearest neighbor lipid shells provides atomistic lipid disruption profile of protein containing lipid membranes.

Authors:  Sara Y Cheng; Hai V Duong; Campbell Compton; Mark W Vaughn; Hoa Nguyen; Kwan H Cheng
Journal:  Biophys Chem       Date:  2015-01-19       Impact factor: 2.352

7.  Characterization of void space in polydisperse sphere packings: Applications to hard-sphere packings and to protein structure analysis.

Authors:  Moumita Maiti; Arun Lakshminarayanan; Srikanth Sastry
Journal:  Eur Phys J E Soft Matter       Date:  2013-01-28       Impact factor: 1.890

8.  Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them.

Authors:  Tanya M Raschke; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-02       Impact factor: 11.205

9.  VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation.

Authors:  Sabrina A Silveira; Alexandre V Fassio; Valdete M Gonçalves-Almeida; Raquel C de Melo-Minardi; Elisa B de Lima; Yussif T Barcelos; Flávia F Aburjaile; Laerte M Rodrigues; Wagner Meira
Journal:  BMC Proc       Date:  2014-08-28

10.  Discrimination of thermophilic and mesophilic proteins.

Authors:  Todd J Taylor; Iosif I Vaisman
Journal:  BMC Struct Biol       Date:  2010-05-17
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