Use of freely available and open source tools for in silico screening in chemical biology

Gareth W. Price; Phillip S. Gould; Andrew Marsh

doi:10.1021/ed400302u

Use of freely available and open source tools for in silico screening in chemical biology

Gareth W. Price, Phillip S. Gould, Andrew Marsh

School of Life Sciences

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

12 Citations (Scopus)

Abstract

Automated computational docking of large libraries of chemical compounds to a protein can aid in pharmaceutical drug design and gives scientists with basic computer experience a tool to help plan wet laboratory investigations when exploring the combination of chemical and pharmacological spaces. The use of open source tools to develop and select ligands for subsequent screening is outlined. A protocol leveraging the power of Open Babel and AutoDock Vina to perform file conversion, minimization, and docking implemented as a Python script is offered.

Original language	English
Pages (from-to)	602-604
Number of pages	3
Journal	Journal of Chemical Education
Volume	91
Issue number	4
DOIs	https://doi.org/10.1021/ed400302u
Publication status	Published - 8 Apr 2014

Keywords

Biochemistry
Chemoinformatics
Collaborative/Cooperative Learning
Discovery Learning
Drugs/Pharmaceuticals
Graduate Education/Research
Medicinal Chemistry
Upper-Division Undergraduate

ASJC Scopus subject areas

Chemistry(all)
Education

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10.1021/ed400302u

Cite this

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abstract = "Automated computational docking of large libraries of chemical compounds to a protein can aid in pharmaceutical drug design and gives scientists with basic computer experience a tool to help plan wet laboratory investigations when exploring the combination of chemical and pharmacological spaces. The use of open source tools to develop and select ligands for subsequent screening is outlined. A protocol leveraging the power of Open Babel and AutoDock Vina to perform file conversion, minimization, and docking implemented as a Python script is offered.",

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AB - Automated computational docking of large libraries of chemical compounds to a protein can aid in pharmaceutical drug design and gives scientists with basic computer experience a tool to help plan wet laboratory investigations when exploring the combination of chemical and pharmacological spaces. The use of open source tools to develop and select ligands for subsequent screening is outlined. A protocol leveraging the power of Open Babel and AutoDock Vina to perform file conversion, minimization, and docking implemented as a Python script is offered.

KW - Biochemistry

KW - Chemoinformatics

KW - Collaborative/Cooperative Learning

KW - Discovery Learning

KW - Drugs/Pharmaceuticals

KW - Graduate Education/Research

KW - Medicinal Chemistry

KW - Upper-Division Undergraduate

U2 - 10.1021/ed400302u

DO - 10.1021/ed400302u

M3 - Article

AN - SCOPUS:84898011058

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JO - Journal of Chemical Education

JF - Journal of Chemical Education

SN - 0021-9584

IS - 4

ER -

Use of freely available and open source tools for in silico screening in chemical biology

Abstract

Keywords

ASJC Scopus subject areas

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Cite this