Covalent docking using autodock: Two‐point attractor and flexible side chain methods
作者： Giulia Bianco , Stefano Forli , David S. Goodsell , Arthur J. Olson
DOI: 10.1002/PRO.2733
关键词: AutoDock 、 Protein–ligand docking 、 Attractor 、 Combinatorial chemistry 、 Side chain 、 Training set 、 Docking (molecular) 、 Covalent bond 、 Searching the conformational space for docking 、 Computer science 、 Computational science
摘要: We describe two methods of automated covalent docking using Autodock4: the two-point attractor method and flexible side chain method. Both were applied to a training set 20 diverse protein-ligand complexes, evaluating their reliability in predicting crystallographic pose ligands. The performed best, recovering 75% cases, with failures for largest inhibitors tested. are freely available at AutoDock website (http://autodock.scripps.edu).
sci-hub.se 参考文章(21)
Christoph Scholz, Sabine Knorr, Kay Hamacher, Boris Schmidt, DOCKTITE-a highly versatile step-by-step workflow for covalent docking and virtual screening in the molecular operating environment. Journal of Chemical Information and Modeling. ,vol. 55, pp. 398- 406 ,(2015) , 10.1021/CI500681R
Kai Zhu, Kenneth W. Borrelli, Jeremy R. Greenwood, Tyler Day, Robert Abel, Ramy S. Farid, Edward Harder, Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring Journal of Chemical Information and Modeling. ,vol. 54, pp. 1932- 1940 ,(2014) , 10.1021/CI500118S
Stefano Forli, Arthur J. Olson, A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. Journal of Medicinal Chemistry. ,vol. 55, pp. 623- 638 ,(2012) , 10.1021/JM2005145
Jesus M. Ontoria, Stefania Di Marco, Immacolata Conte, M. Emilia Di Francesco, Cristina Gardelli, Uwe Koch, Victor G. Matassa, Marco Poma, Christian Steinkühler, Cinzia Volpari, Steven Harper, The Design and Enzyme-Bound Crystal Structure of Indoline Based Peptidomimetic Inhibitors of Hepatitis C Virus NS3 Protease Journal of Medicinal Chemistry. ,vol. 47, pp. 6443- 6446 ,(2004) , 10.1021/JM049435D
Brian Shoichet, Jack Taunton, N London, RM Miller, S Krishnan, K Uchida, JJ Irwin, O Eidam, L Gibold, P Cimermančič, R Bonnet, BK Shoichet, Covalent docking of large libraries for the discovery of chemical probes Nature Chemical Biology. ,vol. 10, pp. 1066- 1072 ,(2014) , 10.1038/NCHEMBIO.1666
Robert Mah, Jason R. Thomas, Cynthia M. Shafer, Drug discovery considerations in the development of covalent inhibitors. Bioorganic & Medicinal Chemistry Letters. ,vol. 24, pp. 33- 39 ,(2014) , 10.1016/J.BMCL.2013.10.003
Nicholas R. Silvaggi, Helen R. Josephine, Alexandre P. Kuzin, Rajesh Nagarajan, R.F. Pratt, Judith A. Kelly, Crystal Structures of Complexes between the R61 DD-peptidase and Peptidoglycan-mimetic β-Lactams: A Non-covalent Complex with a “Perfect Penicillin” Journal of Molecular Biology. ,vol. 345, pp. 521- 533 ,(2005) , 10.1016/J.JMB.2004.10.076
Juswinder Singh, Russell C. Petter, Thomas A. Baillie, Adrian Whitty, The resurgence of covalent drugs Nature Reviews Drug Discovery. ,vol. 10, pp. 307- 317 ,(2011) , 10.1038/NRD3410
Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson, AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins. Journal of Chemical Information and Modeling. ,vol. 54, pp. 2371- 2379 ,(2014) , 10.1021/CI500209E
Xuchang Ouyang, Shuo Zhou, Chinh Tran To Su, Zemei Ge, Runtao Li, Chee Keong Kwoh, CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints Journal of Computational Chemistry. ,vol. 34, pp. 326- 336 ,(2013) , 10.1002/JCC.23136