Automated docking of peptides and proteins by genetic algorithm

Junmei Wang; Tingjun Hou; Lirong Chen; Xiaojie Xu

doi:10.1016/S0169-7439(98)00132-4

Automated docking of peptides and proteins by genetic algorithm

Junmei Wang, Tingjun Hou, Lirong Chen, Xiaojie Xu

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

Genetic algorithm (GA) combined with random search has been applied to thoroughly search the appropriate associated sites for both peptide and protein complexes. Steric complementarity and energetic complementarity of ligand with its receptor have been separately considered in our two-stage automated docking. Eight complexes have been randomly selected from the Protein Data Bank to test our procedure. Conformations and orientations close to the crystallographically determined structures are obtained. For most cases, the smallest RMS (root mean square of distance) of the GA solutions is smaller than 1.0.

Original language	English (US)
Pages (from-to)	281-286
Number of pages	6
Journal	Chemometrics and Intelligent Laboratory Systems
Volume	45
Issue number	1-2
DOIs	https://doi.org/10.1016/S0169-7439(98)00132-4
State	Published - Jan 18 1999

Keywords

Automated docking
Genetic algorithm
Random searching

ASJC Scopus subject areas

Analytical Chemistry
Software
Process Chemistry and Technology
Spectroscopy
Computer Science Applications

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10.1016/S0169-7439(98)00132-4

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title = "Automated docking of peptides and proteins by genetic algorithm",

abstract = "Genetic algorithm (GA) combined with random search has been applied to thoroughly search the appropriate associated sites for both peptide and protein complexes. Steric complementarity and energetic complementarity of ligand with its receptor have been separately considered in our two-stage automated docking. Eight complexes have been randomly selected from the Protein Data Bank to test our procedure. Conformations and orientations close to the crystallographically determined structures are obtained. For most cases, the smallest RMS (root mean square of distance) of the GA solutions is smaller than 1.0.",

keywords = "Automated docking, Genetic algorithm, Random searching",

author = "Junmei Wang and Tingjun Hou and Lirong Chen and Xiaojie Xu",

note = "Funding Information: This project was supported by NSFC 29573095.",

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AU - Wang, Junmei

AU - Hou, Tingjun

AU - Chen, Lirong

AU - Xu, Xiaojie

N1 - Funding Information: This project was supported by NSFC 29573095.

PY - 1999/1/18

Y1 - 1999/1/18

N2 - Genetic algorithm (GA) combined with random search has been applied to thoroughly search the appropriate associated sites for both peptide and protein complexes. Steric complementarity and energetic complementarity of ligand with its receptor have been separately considered in our two-stage automated docking. Eight complexes have been randomly selected from the Protein Data Bank to test our procedure. Conformations and orientations close to the crystallographically determined structures are obtained. For most cases, the smallest RMS (root mean square of distance) of the GA solutions is smaller than 1.0.

AB - Genetic algorithm (GA) combined with random search has been applied to thoroughly search the appropriate associated sites for both peptide and protein complexes. Steric complementarity and energetic complementarity of ligand with its receptor have been separately considered in our two-stage automated docking. Eight complexes have been randomly selected from the Protein Data Bank to test our procedure. Conformations and orientations close to the crystallographically determined structures are obtained. For most cases, the smallest RMS (root mean square of distance) of the GA solutions is smaller than 1.0.

KW - Automated docking

KW - Genetic algorithm

KW - Random searching

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Automated docking of peptides and proteins by genetic algorithm

Abstract

Keywords

ASJC Scopus subject areas

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