Abstract
Protein-ligand docking is currently an important tool in drug discovery efforts and an active area of research that has been the subject of important developments over the last decade. These are well portrayed in the rising number of available protein-ligand docking software programs, increasing level of sophistication of its most recent applications, and growing number of users. While starting by summarizing the key concepts in protein-ligand docking, this article presents an analysis of the evolution of this important field of research over the past decade. Particular attention is given to the massive range of alternatives, in terms of protein-ligand docking software programs currently available. The emerging trends in this field are the subject of special attention, while old established docking alternatives are critically revisited. Current challenges in the field of protein-ligand docking such as the treatment of protein flexibility, the presence of structural water molecules and its effect in docking, and the entropy of binding are dissected and discussed, trying to anticipate the next years in the field.
Keywords: Docking, drug design, entropy, flexibility, scoring, software, virtual Screening.
Current Medicinal Chemistry
Title:Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field
Volume: 20 Issue: 18
Author(s): S.F. Sousa, A.J.M. Ribeiro, J.T.S. Coimbra, R.P.P. Neves, S.A. Martins, N.S.H.N. Moorthy, P.A. Fernandes and M.J. Ramos
Affiliation:
Keywords: Docking, drug design, entropy, flexibility, scoring, software, virtual Screening.
Abstract: Protein-ligand docking is currently an important tool in drug discovery efforts and an active area of research that has been the subject of important developments over the last decade. These are well portrayed in the rising number of available protein-ligand docking software programs, increasing level of sophistication of its most recent applications, and growing number of users. While starting by summarizing the key concepts in protein-ligand docking, this article presents an analysis of the evolution of this important field of research over the past decade. Particular attention is given to the massive range of alternatives, in terms of protein-ligand docking software programs currently available. The emerging trends in this field are the subject of special attention, while old established docking alternatives are critically revisited. Current challenges in the field of protein-ligand docking such as the treatment of protein flexibility, the presence of structural water molecules and its effect in docking, and the entropy of binding are dissected and discussed, trying to anticipate the next years in the field.
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Sousa S.F., Ribeiro A.J.M., Coimbra J.T.S., Neves R.P.P., Martins S.A., Moorthy N.S.H.N., Fernandes P.A. and Ramos M.J., Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field, Current Medicinal Chemistry 2013; 20 (18) . https://dx.doi.org/10.2174/0929867311320180002
DOI https://dx.doi.org/10.2174/0929867311320180002 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
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