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.
read more
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...
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Controlling the Circadian Clock with High Temporal Resolution through Photodosing.
Dušan Kolarski,Akiko Sugiyama,Ghislain Breton,Christin Rakers,Daisuke Ono,Albert Schulte,Florence Tama,Kenichiro Itami,Wiktor Szymanski,Wiktor Szymanski,Tsuyoshi Hirota,Ben L. Feringa +11 more
TL;DR: This research paves the way for the application of photodosing in achieving precise temporal control over the biological timing and opens the door for chronophotopharmacology to deeper understand the circadian clock system.
Identification of potential HIV-1 integrase strand transfer inhibitors: in silico virtual screening and QM/MM docking studies.
TL;DR: The pharmacophore hypothesis AADHR was used as a 3D query in a sequential virtual screening study to filter small molecule databases Maybridge, ChemBridge and Asinex and found three compounds that form stable interactions with key residues.
41
Design, synthesis and molecular docking of pyrazolo [3,4d] thiazole hybrids as potential anti-HIV-1 NNRT inhibitors.
TL;DR: A series of pyrazolo[3.4,d,d]thiazole hybrids 6 were synthesized from 5-arylidene-2-imino-3-(4-arylthiazol- 2-yl)-thiazolidin-4-ones 5 and found that these compounds might have potent RT inhibition activity.
41
Substrate-assisted catalytic mechanism of O-GlcNAc transferase discovered by quantum mechanics/molecular mechanics investigation.
TL;DR: The catalytic mechanism of this metal-independent glycosyltransferase is investigated here using QM(DFT)/MM methods, and the existence of a concerted S(N)2-like mechanism, in which a nucleophilic attack by O(Ser) is facilitated by proton transfer to the catalytic base and the dissociation of the leaving group occur almost simultaneously.
41
What in silico molecular docking can do for the 'bench-working biologists'.
TL;DR: This mini-review attempts to present the docking problem and available solutions from a non-bioinformatician point of view and makes a selection of the available servers and programs.
41
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.
Development and validation of a genetic algorithm for flexible docking.
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.
6.5K
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.
2.8K
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.
1.7K
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.
1.3K