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 | |
| Publication status | Published - 8 Apr 2014 |
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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
Cite this
Use of freely available and open source tools for in silico screening in chemical biology. / Price, Gareth W.; Gould, Phillip S.; Marsh, Andrew.
In: Journal of Chemical Education, Vol. 91, No. 4, 08.04.2014, p. 602-604.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Use of freely available and open source tools for in silico screening in chemical biology
AU - Price, Gareth W.
AU - Gould, Phillip S.
AU - Marsh, Andrew
PY - 2014/4/8
Y1 - 2014/4/8
N2 - 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.
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
VL - 91
SP - 602
EP - 604
JO - Journal of Chemical Education
JF - Journal of Chemical Education
SN - 0021-9584
IS - 4
ER -