Journal Article10.1021/JM0306430
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
Richard A. Friesner,Jay L. Banks,Robert B. Murphy,Thomas A. Halgren,Jasna Klicic,Daniel T. Mainz,Matthew P. Repasky,Eric H. Knoll,Mee Shelley,Jason K. Perry,David E. Shaw,Perry Francis,Peter S Shenkin +12 more
TL;DR: Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand to find the best docked pose using a model energy function that combines empirical and force-field-based terms.
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Abstract: Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose Errors in geometry for the top-ranked pose are less than 1 A in nearly ha
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Citations
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
Thomas A. Halgren,Robert B. Murphy,Richard A. Friesner,Hege S. Beard,Leah L. Frye,W. Thomas Pollard,Jay L. Banks +6 more
TL;DR: Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
Richard A. Friesner,Robert B. Murphy,Matthew P. Repasky,Leah L. Frye,Jeremy R. Greenwood,Thomas A. Halgren,Paul C. Sanschagrin,Daniel T. Mainz +7 more
TL;DR: Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
TL;DR: It is shown that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets.
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Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors
Zhenming Jin,Zhenming Jin,Xiaoyu Du,Yechun Xu,Yong-Qiang Deng,Meiqin Liu,Yao Zhao,Bing Zhang,Xiaofeng Li,Leike Zhang,Chao Peng,Yinkai Duan,Jing Yu,Lin Wang,Kailin Yang,Fengjiang Liu,Ren-Di Jiang,Xing-Lou Yang,Tian You,Liu X,Xiuna Yang,Fang Bai,Hong Liu,Xiang Liu,Luke W. Guddat,Wenqing Xu,Wenqing Xu,Gengfu Xiao,Cheng-Feng Qin,Zhengli Shi,Hualiang Jiang,Hualiang Jiang,Zihe Rao,Zihe Rao,Zihe Rao,Haitao Yang +35 more
TL;DR: A programme of structure-assisted drug design and high-throughput screening identifies six compounds that inhibit the main protease of SARS-CoV-2, demonstrating the ability of this strategy to isolate drug leads with clinical potential.
Docking and scoring in virtual screening for drug discovery: methods and applications.
TL;DR: Key concepts and specific features of small-molecule–protein docking methods are reviewed, selected applications are highlighted and recent advances that aim to address the acknowledged limitations of established approaches are discussed.
References
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TL;DR: A new shape-based method for accurately docking ligands into protein active sites, LigandFit, which appears quite promising, reproducing the X-ray structure ligand pose within an RMS of 2A in 14 out of the 19 complexes.
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TL;DR: The outcomes of this project have been organized into a Web-accessible database named the PDBbind database and led to a collection of binding affinity data (K(d), K(i), and IC(50) for a total of 1359 complexes.
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TL;DR: A test of FLEXX, a fully automatic docking tool for flexible ligands, on a highly diverse data set of 200 protein–ligand complexes from the Protein Data Bank, finds that 46.5% of the complexes of the data set can be reproduced by a FLE XX docking solution at rank 1 with an rms deviation from the observed structure.
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