Journal Article10.1021/JM030644S
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.
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Abstract: Glide's ability to identify active compounds in a database screen is characterized by applying Glide to a diverse set of nine protein receptors. In many cases, two, or even three, protein sites are employed to probe the sensitivity of the results to the site geometry. To make the database screens as realistic as possible, the screens use sets of “druglike” decoy ligands that have been selected to be representative of what we believe is likely to be found in the compound collection of a pharmaceutical or biotechnology company. Results are presented for releases 1.8, 2.0, and 2.5 of Glide. The comparisons show that average measures for both “early” and “global” enrichment for Glide 2.5 are 3 times higher than for Glide 1.8 and more than 2 times higher than for Glide 2.0 because of better results for the least well-handled screens. This improvement in enrichment stems largely from the better balance of the more widely parametrized GlideScore 2.5 function and the inclusion of terms that penalize ligand−protei...
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Citations
Computational strategy for intrinsically disordered protein ligand design leads to the discovery of p53 transactivation domain I binding compounds that activate the p53 pathway
Hao Ruan,Chen Yu,Xiaogang Niu,Weilin Zhang,Hanzhong Liu,Limin Chen,Ruoyao Xiong,Qi Sun,Changwen Jin,Ying Liu,Luhua Lai +10 more
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Applying Small Molecule Signal Transducer and Activator of Transcription-3 (STAT3) Protein Inhibitors as Pancreatic Cancer Therapeutics
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TL;DR: PG-S3-001, a small molecule derived from the SH-4-54 class of STAT3 inhibitors, was found to inhibit patient-derived pancreatic cancer cell proliferation in vitro and in vivo in the low micromolar range.
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Affinity of Aporphines for the Human 5-HT2A Receptor: Insights from Homology Modeling and Molecular Docking Studies
Stevan Pecic,Pooja Makkar,Sandeep Chaudhary,Boojala Vijay B. Reddy,Hernán A. Navarro,Wayne W. Harding +5 more
TL;DR: Ser242, Phe234, and Gly238 are identified as key residues responsible for the affinity of these compounds for the 5-HT(2A) receptor.
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In silico modelling and molecular dynamics simulation studies of thiazolidine based PTP1B inhibitors
TL;DR: The present investigation has identified some of the indispensible structural features of thiazolidine analogues which can further be explored to optimize PTP1B inhibitors.
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Multiple ligand docking by Glide: implications for virtual second-site screening
TL;DR: The HSP90 subset from real life fragment optimization programs revealed that Glide is able to reproduce the positions of multiple bound fragments if conserved water molecules are considered and the utility of Glide in sequential multiple docking applications is assessed.
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References
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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TL;DR: GOLD (Genetic Optimisation for Ligand Docking) is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding.
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
TL;DR: A simple empirical scoring function designed to estimate the free energy of binding for aprotein–ligand complex when the 3D structure of the complex is known or can be approximated and it is compared to approaches by other workers.
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Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine.
TL;DR: Results are presented evaluating reliability and accuracy of dockings compared with crystallographic experimental results on 81 protein/ligand pairs of substantial structural diversity, and assessing Surflex's utility as a screening tool on two protein targets using data sets on which competing methods were run.
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