title: Protein-ligand docking in the new millennium--a retrospective of 10 years in the field.
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.
authors.affiliation: REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
authors.forename: S F
authors.initials: SF
authors.lastname: Sousa
authors.forename: A J M
authors.initials: AJ
authors.lastname: Ribeiro
authors.forename: J T S
authors.initials: JT
authors.lastname: Coimbra
authors.forename: R P P
authors.initials: RP
authors.lastname: Neves
authors.forename: S A
authors.initials: SA
authors.lastname: Martins
authors.forename: N S H N
authors.initials: NS
authors.lastname: Moorthy
authors.forename: P A
authors.initials: PA
authors.lastname: Fernandes
authors.forename: M J
authors.initials: MJ
authors.lastname: Ramos
mesh_terms: D000818:Animals; D015195:Drug Design; D019277:Entropy; D049674:History, 21st Century; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation / Q000266:history; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins