Abstract
| Original language | English |
|---|---|
| Pages (from-to) | 1117-1126 |
| Number of pages | 10 |
| Journal | Journal of Computational Chemistry |
| Volume | 25 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 15 Jul 2004 |
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Evaluation of the Protein Solvent-Accessible Surface Using Reduced Representations in terms of Critical Points of the Electron Density. / Becue, Andy; Meurice, Nathalie; Leherte, Laurence; Vercauteren, Daniel.
In: Journal of Computational Chemistry, Vol. 25, No. 9, 15.07.2004, p. 1117-1126.Research output: Contribution to journal › Article
TY - JOUR
T1 - Evaluation of the Protein Solvent-Accessible Surface Using Reduced Representations in terms of Critical Points of the Electron Density
AU - Becue, Andy
AU - Meurice, Nathalie
AU - Leherte, Laurence
AU - Vercauteren, Daniel
N1 - Copyright 2008 Elsevier B.V., All rights reserved.
PY - 2004/7/15
Y1 - 2004/7/15
N2 - The aim of our study is the development of a method for calculating the interface of dimerization of protein-protein complexes based on simplified medium-resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent-Accessible Surface Area (SASA) of macromolecules could be applied to medium-resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 Å crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side-chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side-chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins.
AB - The aim of our study is the development of a method for calculating the interface of dimerization of protein-protein complexes based on simplified medium-resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent-Accessible Surface Area (SASA) of macromolecules could be applied to medium-resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 Å crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side-chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side-chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins.
UR - http://www.scopus.com/inward/record.url?scp=2942588638&partnerID=8YFLogxK
U2 - 10.1002/jcc.20033
DO - 10.1002/jcc.20033
M3 - Article
AN - SCOPUS:2942588638
VL - 25
SP - 1117
EP - 1126
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
SN - 0192-8651
IS - 9
ER -