Efficient docking of peptides to proteins without prior knowledge of the binding site.

ABSTRACT: Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein-protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different protein/ligand complexes for which the structure was known, without prior knowledge of the binding site. More specifically, we look at factors influencing the accuracy of the final structure, such as the number of torsional degrees of freedom in the ligand. We conclude that the Autodock program packag

SUBMITTER: Hetenyi C 

PROVIDER: S-EPMC2373668 | biostudies-literature | 2002 Jul

REPOSITORIES: biostudies-literature