<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Miguel L. Teodoro</style></author><author><style face="normal" font="default" size="100%">George N. Phillips Jr.</style></author><author><style face="normal" font="default" size="100%">L. E. Kavraki</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular Docking: A Problem with Thousands of                  Degrees of Freedom</style></title><secondary-title><style face="normal" font="default" size="100%">Proc. of the 2001 IEEE International Conference on                  Robotics and Automation (ICRA 2001)</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">computer-assisted drug design</style></keyword><keyword><style  face="normal" font="default" size="100%">kavrakilab</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2001</style></year><pub-dates><date><style  face="normal" font="default" size="100%">May</style></date></pub-dates></dates><publisher><style face="normal" font="default" size="100%">IEEE press</style></publisher><pub-location><style face="normal" font="default" size="100%">Seoul, Korea</style></pub-location><pages><style face="normal" font="default" size="100%">960-966</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This paper reports on the problem of docking a highly flexible small molecule to the pocket of a highly flexible receptor macromolecule. The prediction of the intermolecular complex is of vital importance for the development of new therapeutics as docking can alter the chemical behavior of the receptor macromolecule. We first present current methods for docking, which have several limitations. Some of these methods consider only the flexibility of the ligand solving a problem with a few tens of degrees of freedom. When the receptor flexibility is taken into account several hundreds or even thousands of degrees of freedom need to be considered. Most methods take into account only a small number of these degrees of freedom by using chemical knowledge specific to the problem. We show how to use a singular value decomposition of molecular dynamics trajectories to automatically obtain information about the global flexibility of the receptor and produce interesting conformations that can be used for docking purposes.</style></abstract><work-type><style face="normal" font="default" size="100%">inproceedings</style></work-type></record></records></xml>
