A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. Export

@article{citeulike:833576, abstract = {We have developed a new docking method to consider receptor flexibility, a hybrid method of molecular dynamics and harmonic dynamics. The global motions of the whole receptor were approximately introduced into those of the receptor in the docking simulation as harmonic dynamics. On the other hand, the local flexibility of the side chains was also considered by conventional molecular dynamics. We confirmed that this new method can reproduce the fluctuations of the whole receptor by making a comparison of the directions and amplitudes of the global fluctuations. Then this method was applied to the docking of HIV-1 protease and its ligand. As a result, we observed a docking process where the ligand enters into the binding pocket well, which implies that this method is effective enough to reproduce a molecular complex formation.}, address = {Japan Biological Information Research Center, Japan Biological Informatics Consortium, Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan. tatsumi@jbirc.aist.go.jp}, author = {Tatsumi, R. and Fukunishi, Y. and Nakamura, H.}, citeulike-article-id = {833576}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.20133}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15473011}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15473011}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/109671853/ABSTRACT}, doi = {10.1002/jcc.20133}, issn = {0192-8651}, journal = {J Comput Chem}, keywords = {flexibility, hd, md}, month = {December}, number = {16}, pages = {1995--2005}, posted-at = {2007-11-23 12:40:52}, priority = {2}, title = {A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.}, url = {http://dx.doi.org/10.1002/jcc.20133}, volume = {25}, year = {2004} }

TY - JOUR ID - citeulike:833576 L3 - citeulike-article-id:833576 N2 - We have developed a new docking method to consider receptor flexibility, a hybrid method of molecular dynamics and harmonic dynamics. The global motions of the whole receptor were approximately introduced into those of the receptor in the docking simulation as harmonic dynamics. On the other hand, the local flexibility of the side chains was also considered by conventional molecular dynamics. We confirmed that this new method can reproduce the fluctuations of the whole receptor by making a comparison of the directions and amplitudes of the global fluctuations. Then this method was applied to the docking of HIV-1 protease and its ligand. As a result, we observed a docking process where the ligand enters into the binding pocket well, which implies that this method is effective enough to reproduce a molecular complex formation. IS - 16 JF - J Comput Chem SN - 0192-8651 AD - Japan Biological Information Research Center, Japan Biological Informatics Consortium, Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan. tatsumi@jbirc.aist.go.jp EP - 2005 TI - A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. VL - 25 SP - 1995 KW - flexibility KW - hd KW - md AU - Tatsumi, R AU - Fukunishi, Y AU - Nakamura, H PY - 2004/12// UR - http://dx.doi.org/10.1002/jcc.20133 ER -