title: Molecular docking and structure-based drug design strategies.
abstract: Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.
authors.affiliation: Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil. leonardo@ifsc.usp.br.
authors.forename: Leonardo G
authors.initials: LG
authors.lastname: Ferreira
authors.affiliation: Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil. rnsantos@ursa.ifsc.usp.br.
authors.forename: Ricardo N
authors.initials: RN
authors.lastname: Dos Santos
authors.affiliation: Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil. oliva@ifsc.usp.br.
authors.forename: Glaucius
authors.initials: G
authors.lastname: Oliva
authors.affiliation: Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil. aandrico@ifsc.usp.br.
authors.forename: Adriano D
authors.initials: AD
authors.lastname: Andricopulo
mesh_terms: D000818:Animals; D015195:Drug Design; D006801:Humans; D062105:Molecular Docking Simulation / Q000379:methods*; D013329:Structure-Activity Relationship
keywords: SBDD; SBVS; drug discovery; molecular interaction; molecular modeling; molecular target; pharmacophore; virtual screening