Scoring Functions for Fragment-Based Drug Discovery
作者： Jui-Chih Wang , Jung-Hsin Lin
DOI: 10.1007/978-1-4939-2486-8_9
关键词:
摘要: Fragment-based drug design represents a challenge for computational because almost inevitably fragments will be weak binders to the biomolecular targets of specific disease, and performances scoring functions are usually poorer than those stronger binders. This protocol describes how predict binding modes affinities towards their partner with our refined AutoDock function incorporating quantum chemical charge model, namely, restrained electrostatic potential (RESP) model. was calibrated by robust regression analysis has been demonstrated perform well general classes protein-ligand interactions (with root-mean square error about 2.1 kcal/mol).
springer.com
sci-hub.st 参考文章(14)
S. B. Shuker, P. J. Hajduk, R. P. Meadows, S. W. Fesik, Discovering High-Affinity Ligands for Proteins: SAR by NMR Science. ,vol. 274, pp. 1531- 1534 ,(1996) , 10.1126/SCIENCE.274.5292.1531
Jui-Chih Wang, Jung-Hsin Lin, Chung-Ming Chen, Alex L. Perryman, Arthur J. Olson, Robust Scoring Functions for Protein-Ligand Interactions with Quantum Chemical Charge Models Journal of Chemical Information and Modeling. ,vol. 51, pp. 2528- 2537 ,(2011) , 10.1021/CI200220V
Gideon Bollag, James Tsai, Jiazhong Zhang, Chao Zhang, Prabha Ibrahim, Keith Nolop, Peter Hirth, Vemurafenib: the first drug approved for BRAF -mutant cancer Nature Reviews Drug Discovery. ,vol. 11, pp. 873- 886 ,(2012) , 10.1038/NRD3847
Ellene H Mashalidis, Paweł Śledź, Steffen Lang, Chris Abell, A three-stage biophysical screening cascade for fragment-based drug discovery Nature Protocols. ,vol. 8, pp. 2309- 2324 ,(2013) , 10.1038/NPROT.2013.130
Jung-Hsin Lin, Alexander L. Perryman, Julie R. Schames, J. Andrew McCammon, The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers. ,vol. 68, pp. 47- 62 ,(2003) , 10.1002/BIP.10218
Jung-Hsin Lin, Alexander L. Perryman, Julie R. Schames, J. Andrew McCammon, Computational drug design accommodating receptor flexibility: the relaxed complex scheme. Journal of the American Chemical Society. ,vol. 124, pp. 5632- 5633 ,(2002) , 10.1021/JA0260162
Jui-Chih Wang, Jung-Hsin Lin, Scoring functions for prediction of protein-ligand interactions. Current Pharmaceutical Design. ,vol. 19, pp. 2174- 2182 ,(2013) , 10.2174/1381612811319120005
Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson, AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Journal of Computational Chemistry. ,vol. 30, pp. 2785- 2791 ,(2009) , 10.1002/JCC.21256
Helen M Berman, Tammy Battistuz, Talapady N Bhat, Wolfgang F Bluhm, Philip E Bourne, Kyle Burkhardt, Zukang Feng, Gary L Gilliland, Lisa Iype, Shri Jain, Phoebe Fagan, Jessica Marvin, David Padilla, Veerasamy Ravichandran, Bohdan Schneider, Narmada Thanki, Helge Weissig, John Westbrook, Christine Zardecki, The Protein Data Bank Nucleic Acids Research. ,vol. 28, pp. 235- 242 ,(2000) , 10.1093/NAR/28.1.235
Anders Åberg, Alan V Wallace, John A Tainer, Elizabeth D Getzoff, Elsa D Garcin, Andrew S Arvai, Robin J Rosenfeld, Matt D Kroeger, Brian R Crane, Gunilla Andersson, Glen Andrews, Peter J Hamley, Philip R Mallinder, David J Nicholls, Stephen A St-Gallay, Alan C Tinker, Nigel P Gensmantel, Antonio Mete, David R Cheshire, Stephen Connolly, Dennis J Stuehr, Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase. Nature Chemical Biology. ,vol. 4, pp. 700- 707 ,(2008) , 10.1038/NCHEMBIO.115