Literature DB >> 19340931

Healthy skepticism: assessing realistic model performance.

Scott P Brown1, Steven W Muchmore, Philip J Hajduk.   

Abstract

Although the development of computational models to aid drug discovery has become an integral part of pharmaceutical research, the application of these models often fails to produce the expected impact on productivity. One reason for this may be that the expected performance of many models is simply not supported by the underlying data, because of often neglected effects of assay and prediction errors on the reliability of the predicted outcome. Another significant challenge to realizing the full potential of computational models is their integration into prospective medicinal chemistry campaigns. This article will analyze the impact of assay and prediction error on model quality, and explore scenarios where computational models can expect to have a significant influence on drug discovery research.

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Year:  2009        PMID: 19340931     DOI: 10.1016/j.drudis.2009.01.012

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  28 in total

1.  Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors.

Authors:  James Luccarelli; Julien Michel; Julian Tirado-Rives; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2010-01-01       Impact factor: 6.006

2.  Fitting and handling dose response data.

Authors:  Gareth Jones
Journal:  J Comput Aided Mol Des       Date:  2014-07-01       Impact factor: 3.686

3.  Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.

Authors:  Samuel Genheden; Ana I Cabedo Martinez; Michael P Criddle; Jonathan W Essex
Journal:  J Comput Aided Mol Des       Date:  2014-02-01       Impact factor: 3.686

Review 4.  Alchemical free energy methods for drug discovery: progress and challenges.

Authors:  John D Chodera; David L Mobley; Michael R Shirts; Richard W Dixon; Kim Branson; Vijay S Pande
Journal:  Curr Opin Struct Biol       Date:  2011-02-23       Impact factor: 6.809

5.  A computational approach for predicting off-target toxicity of antiviral ribonucleoside analogues to mitochondrial RNA polymerase.

Authors:  Holly Freedman; Philip Winter; Jack Tuszynski; D Lorne Tyrrell; Michael Houghton
Journal:  J Biol Chem       Date:  2018-05-08       Impact factor: 5.157

6.  Check your confidence: size really does matter.

Authors:  Heather A Carlson
Journal:  J Chem Inf Model       Date:  2013-08-08       Impact factor: 4.956

7.  Relative Binding Free Energy Calculations Applied to Protein Homology Models.

Authors:  Daniel Cappel; Michelle Lynn Hall; Eelke B Lenselink; Thijs Beuming; Jun Qi; James Bradner; Woody Sherman
Journal:  J Chem Inf Model       Date:  2016-11-18       Impact factor: 4.956

8.  D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.

Authors:  Symon Gathiaka; Shuai Liu; Michael Chiu; Huanwang Yang; Jeanne A Stuckey; You Na Kang; Jim Delproposto; Ginger Kubish; James B Dunbar; Heather A Carlson; Stephen K Burley; W Patrick Walters; Rommie E Amaro; Victoria A Feher; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2016-09-30       Impact factor: 3.686

9.  Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors.

Authors:  Zoltán Orgován; György G Ferenczy; Thomas Steinbrecher; Bence Szilágyi; Dávid Bajusz; György M Keserű
Journal:  J Comput Aided Mol Des       Date:  2018-01-15       Impact factor: 3.686

Review 10.  Rethinking drug design in the artificial intelligence era.

Authors:  Petra Schneider; W Patrick Walters; Alleyn T Plowright; Norman Sieroka; Jennifer Listgarten; Robert A Goodnow; Jasmin Fisher; Johanna M Jansen; José S Duca; Thomas S Rush; Matthias Zentgraf; John Edward Hill; Elizabeth Krutoholow; Matthias Kohler; Jeff Blaney; Kimito Funatsu; Chris Luebkemann; Gisbert Schneider
Journal:  Nat Rev Drug Discov       Date:  2019-12-04       Impact factor: 84.694

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