title: MADAMM: a multistaged docking with an automated molecular modeling protocol.
abstract: Dealing with receptor flexibility in docking methodology is still a problem. The main reason behind this difficulty is the large number of degrees of freedom that have to be considered in this kind of calculations. In this paper, we present an automated procedure, called MADAMM, that allows flexibilization of both the receptor and the ligand during a multistaged docking with an automated molecular modeling protocol. We show that the orientation of particular residues at the interface between the protein and the ligand have a crucial influence on the way they interact during the docking process, and the standard docking methodologies failed to predict their correct mode of binding. We present some examples that demonstrate the capabilities of this approach when compared with traditional docking methodologies.
authors.affiliation: REQUIMTE, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
authors.forename: N M F S A
authors.initials: NM
authors.lastname: Cerqueira
authors.forename: N F
authors.initials: NF
authors.lastname: Bras
authors.forename: P A
authors.initials: PA
authors.lastname: Fernandes
authors.forename: M J
authors.initials: MJ
authors.lastname: Ramos
mesh_terms: D000465:Algorithms; D000911:Antibodies, Monoclonal / Q000276:immunology / Q000378:metabolism; D001665:Binding Sites; D002241:Carbohydrates / Q000737:chemistry; D044603:Cellulosomes / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D018844:Cyclin-Dependent Kinases / Q000378:metabolism; D008024:Ligands; D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D008958:Models, Molecular; D011374:Progesterone / Q000276:immunology; D011485:Protein Binding
chemical_list: D000911:Antibodies, Monoclonal; D002241:Carbohydrates; D008024:Ligands; D011374:Progesterone; D018844:Cyclin-Dependent Kinases; D020928:Mitogen-Activated Protein Kinases