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Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. (Carlsson Lab.)ORCID iD: 0000-0002-4831-3423
2018 (English)In: Rational Drug Design: Methods and Protocols / [ed] Thomas Mavromoustakos; Tahsin F. Kellici, New York, NY: Humana Press, 2018, p. 67-88Chapter in book (Refereed)
Abstract [en]

Main goal in drug discovery is the identification of drug-like compounds capable to modulate specific biological targets. Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key step to be pursued in structure-based drug design (SBDD). Since the increasing number of resolved three-dimensional ligand-protein structures, together with the expansion of computational power and software development, the comprehensive and systematic use of experimental data can be proficiently employed to validate the docking performance. This allows to select and refine the protocol to adopt when predicting the binding pose of trial compounds in a target. Given the availability of multiple docking software, a comparative docking assessment in an early research stage represents a must-use step to minimize fails in molecular modeling. This chapter describes how to perform a docking assessment, using freely available tools, in a semiautomated fashion.

Place, publisher, year, edition, pages
New York, NY: Humana Press, 2018. p. 67-88
Series
Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029
Keywords [en]
Drug design, Drug discovery, Molecular docking, Molecular modeling, Docking assessment, Structure-based drug design (SBDD)
National Category
Theoretical Chemistry Bioinformatics (Computational Biology) Medicinal Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-356420DOI: 10.1007/978-1-4939-8630-9_5PubMedID: 30039402ISBN: 978-1-4939-8629-3 (print)ISBN: 978-1-4939-8630-9 (electronic)OAI: oai:DiVA.org:uu-356420DiVA, id: diva2:1235689
Available from: 2018-07-26 Created: 2018-07-26 Last updated: 2018-10-11Bibliographically approved

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