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Software for molecular docking: a review

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dc.contributor.author Pagadala, Nataraj S.
dc.contributor.author Syed, Khajamohiddin
dc.contributor.author Tuszynski, Jack
dc.date.accessioned 2018-10-25T07:50:52Z
dc.date.available 2018-10-25T07:50:52Z
dc.date.issued 2017
dc.identifier.uri http://hdl.handle.net/11462/1723
dc.description Publshed Article en_US
dc.description.abstract Molecular docking methodology explores the behavior of small molecules in the binding site of a target protein. As more protein structures are determined experimentally using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, molecular docking is increasingly used as a tool in drug discovery. Docking against homologymodeled targets also becomes possible for proteins whose structures are not known. With the docking strategies, the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes. Molecular docking programs perform a search algorithm in which the conformation of the ligand is evaluated recursively until the convergence to the minimum energy is reached. Finally, an affinity scoring function, ΔG [U total in kcal/mol], is employed to rank the candidate poses as the sum of the electrostatic and van der Waals energies. The driving forces for these specific interactions in biological systems aim toward complementarities between the shape and electrostatics of the binding site surfaces and the ligand or substrate. en_US
dc.format.extent 355 236 bytes, 1 file
dc.format.mimetype Application/PDF
dc.language.iso en_US en_US
dc.publisher Biophysical Reviews en_US
dc.relation.ispartofseries Volume 9;Issue 2
dc.subject Rigid body docking en_US
dc.subject Flexible docking en_US
dc.subject Docking accuracy en_US
dc.title Software for molecular docking: a review en_US
dc.type Article en_US

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