A Flexible Approach to Induced Fit Docking Export

@article{citeulike:2014690, abstract = {Abstract: We present Fleksy, a new approach to consider both ligand and receptor flexibility in small molecule docking. Pivotal to our method is the use of a receptor ensemble to describe protein flexibility. To construct these ensembles, we use a backbone-dependent rotamer library and implement the concept of interaction sampling. The latter allows the evaluation of different orientations of ambivalent interaction partners. The docking stage consists of an ensemble-based soft-docking experiment using FlexX-Ensemble, followed by an effective flexible receptorligand complex optimization using Yasara. Fleksy produces a set of receptorligand complexes ranked using a consensus scoring function combining docking scores and force field energies. Averaged over three cross-docking datasets, containing 35 different receptorligand complexes in total, Fleksy reproduces the observed binding mode within 2.0 \r{A} for 78\% of the complexes. This compares favorably to the rigid receptor FlexX program, which on average reaches a success rate of 44\% for these datasets.}, address = {Center for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands, and Department of Molecular Design and Informatics, N.V. Organon, Oss, The Netherlands}, author = {Nabuurs, Sander B. and Wagener, Markus and de Vlieg, Jacob}, citeulike-article-id = {2014690}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/jm070593p}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/jm070593p}, day = {22}, doi = {10.1021/jm070593p}, journal = {J. Med. Chem.}, keywords = {docking, docking\_prog, fleksy}, month = {November}, posted-at = {2008-12-02 16:03:45}, priority = {2}, title = {A Flexible Approach to Induced Fit Docking}, url = {http://dx.doi.org/10.1021/jm070593p}, year = {2007} }

TY - JOUR ID - citeulike:2014690 L3 - citeulike-article-id:2014690 N2 - Abstract: We present Fleksy, a new approach to consider both ligand and receptor flexibility in small molecule docking. Pivotal to our method is the use of a receptor ensemble to describe protein flexibility. To construct these ensembles, we use a backbone-dependent rotamer library and implement the concept of interaction sampling. The latter allows the evaluation of different orientations of ambivalent interaction partners. The docking stage consists of an ensemble-based soft-docking experiment using FlexX-Ensemble, followed by an effective flexible receptorligand complex optimization using Yasara. Fleksy produces a set of receptorligand complexes ranked using a consensus scoring function combining docking scores and force field energies. Averaged over three cross-docking datasets, containing 35 different receptorligand complexes in total, Fleksy reproduces the observed binding mode within 2.0 Å for 78% of the complexes. This compares favorably to the rigid receptor FlexX program, which on average reaches a success rate of 44% for these datasets. JF - J. Med. Chem. AD - Center for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands, and Department of Molecular Design and Informatics, N.V. Organon, Oss, The Netherlands TI - A Flexible Approach to Induced Fit Docking KW - docking KW - docking_prog KW - fleksy AU - Nabuurs, Sander AU - Wagener, Markus AU - de Vlieg, Jacob PY - 2007/11/22/ UR - http://dx.doi.org/10.1021/jm070593p ER -