Literature DB >> 23242264

RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules.

Jed Zaretzki1, Charles Bergeron, Tao-wei Huang, Patrik Rydberg, S Joshua Swamidass, Curt M Breneman.   

Abstract

SUMMARY: Regioselectivity-WebPredictor (RS-WebPredictor) is a server that predicts isozyme-specific cytochrome P450 (CYP)-mediated sites of metabolism (SOMs) on drug-like molecules. Predictions may be made for the promiscuous 2C9, 2D6 and 3A4 CYP isozymes, as well as CYPs 1A2, 2A6, 2B6, 2C8, 2C19 and 2E1. RS-WebPredictor is the first freely accessible server that predicts the regioselectivity of the last six isozymes. Server execution time is fast, taking on average 2s to encode a submitted molecule and 1s to apply a given model, allowing for high-throughput use in lead optimization projects. AVAILABILITY: RS-WebPredictor is accessible for free use at http://reccr.chem.rpi.edu/Software/RS-WebPredictor/

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Year:  2012        PMID: 23242264      PMCID: PMC3570214          DOI: 10.1093/bioinformatics/bts705

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  6 in total

1.  Fast bundle algorithm for multiple-instance learning.

Authors:  Charles Bergeron; Gregory Moore; Jed Zaretzki; Curt M Breneman; Kristin P Bennett
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  2012-06       Impact factor: 6.226

2.  The SMARTCyp cytochrome P450 metabolism prediction server.

Authors:  Patrik Rydberg; David E Gloriam; Lars Olsen
Journal:  Bioinformatics       Date:  2010-10-14       Impact factor: 6.937

Review 3.  Clinical importance of the cytochromes P450.

Authors:  Daniel W Nebert; David W Russell
Journal:  Lancet       Date:  2002-10-12       Impact factor: 79.321

4.  RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes.

Authors:  Jed Zaretzki; Patrik Rydberg; Charles Bergeron; Kristin P Bennett; Lars Olsen; Curt M Breneman
Journal:  J Chem Inf Model       Date:  2012-05-29       Impact factor: 4.956

5.  RS-predictor: a new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4.

Authors:  Jed Zaretzki; Charles Bergeron; Patrik Rydberg; Tao-wei Huang; Kristin P Bennett; Curt M Breneman
Journal:  J Chem Inf Model       Date:  2011-06-15       Impact factor: 4.956

Review 6.  Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms.

Authors:  Johannes Kirchmair; Mark J Williamson; Jonathan D Tyzack; Lu Tan; Peter J Bond; Andreas Bender; Robert C Glen
Journal:  J Chem Inf Model       Date:  2012-02-17       Impact factor: 4.956

  6 in total
  8 in total

Review 1.  Predicting drug metabolism: experiment and/or computation?

Authors:  Johannes Kirchmair; Andreas H Göller; Dieter Lang; Jens Kunze; Bernard Testa; Ian D Wilson; Robert C Glen; Gisbert Schneider
Journal:  Nat Rev Drug Discov       Date:  2015-04-24       Impact factor: 84.694

2.  Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism.

Authors:  Tyler B Hughes; S Joshua Swamidass
Journal:  Chem Res Toxicol       Date:  2017-02-02       Impact factor: 3.739

3.  NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism.

Authors:  Anush Chiappino-Pepe; Kiandokht Haddadi; Homa MohammadiPeyhani; Jasmin Hafner; Noushin Hadadi; Vassily Hatzimanikatis
Journal:  Elife       Date:  2021-08-03       Impact factor: 8.140

4.  Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics.

Authors:  Anastasia V Rudik; Alexander V Dmitriev; Alexey A Lagunin; Dmitry A Filimonov; Vladimir V Poroikov
Journal:  J Cheminform       Date:  2016-11-28       Impact factor: 5.514

5.  Screening, molecular simulation & in silico kinetics of virtually designed covid-19 main protease inhibitors.

Authors:  Mohammed S Aleissa; Mohammed Al-Zharani; Md Saquib Hasnain; Saad Alkahtani
Journal:  J King Saud Univ Sci       Date:  2022-08-31

6.  Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites.

Authors:  Tyler B Hughes; Na Le Dang; Ayush Kumar; Noah R Flynn; S Joshua Swamidass
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

7.  A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota.

Authors:  Ashok K Sharma; Shubham K Jaiswal; Nikhil Chaudhary; Vineet K Sharma
Journal:  Sci Rep       Date:  2017-08-29       Impact factor: 4.379

Review 8.  Computational methods for drug design and discovery: focus on China.

Authors:  Mingyue Zheng; Xian Liu; Yuan Xu; Honglin Li; Cheng Luo; Hualiang Jiang
Journal:  Trends Pharmacol Sci       Date:  2013-09-11       Impact factor: 14.819

  8 in total

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