title: Automated docking for novel drug discovery.
abstract: BACKGROUND
  The volume of three-dimensional structural information of macromolecules and the number of computational tools to predict binding modes and affinities of molecular complexes are increasing daily. Molecular docking is a rational structural approach employed to predict thermodynamic parameters based on molecular recognition between two or more molecules. In addition, docking studies have become very important for therapeutic applications in modern structure-based drug design because this computational tool uses few economic resources. However, they omit many biological conditions that critically influence small and macromolecular structural motions. To mimic physiological conditions, it is necessary to consider other environmental factors, such as the presence of water molecules and the flexibility of ligands and side chain residues of proteins. Furthermore, molecular dynamics simulations have been coupled with docking procedures to expand the boundaries and obtain more reliable information.
  
  
  METHODS
  In this article, we review current advances in protein-small molecule docking and possible future directions.
  
  
  CONCLUSIONS
  Docking studies include many conformations to predict binding free energies (scoring functions) and to search (scoring sampling) for the most representative binding conformations. Therefore, several biological properties, from side chain residues to complete protein motions, have been included in docking studies to improve theoretical predictions.
authors: Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México. jcorreab@ipn.mx
authors: Martiniano
authors: M
authors: Bello
authors: Marlet
authors: M
authors: Martínez-Archundia
authors: José
authors: J
authors: Correa-Basurto
mesh_terms: D000465:Algorithms; D055808:Drug Discovery / Q000379:methods*; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011506:Proteins / Q000378:metabolism*
chemical_list: D008024:Ligands; D011506:Proteins