MADAMM: A multistaged docking with an automated molecular modeling protocol

• Type: Article in International Scientific Journal
• Date: 2009

Authors

Cerqueira, NMFSA (Author) FCUP; Bras, NF (Author) Other; Fernandes, PA (Author) FCUP; Ramos, MJ (Author) FCUP

Journal

Title: Proteins: Structure, Function and Genetics

Vol. 74

Pages: 192-206

ISSN: 0887-3585

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 23 Citations

Scopus - 29 Citations

Scientific classification

FOS: Natural sciences > Biological sciences

Other information

Authenticus ID: P-003-RWZ

DOI: 10.1002/prot.22146

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 15