Literature DB >> 22246296

The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years.

Terry Richard Stouch1.   

Abstract

The future of the advancement as well as the reputation of computer-aided drug design will be guided by a more thorough understanding of the domain of applicability of our methods and the errors and confidence intervals of their results. The implications of error in current force fields applied to drug design are given are given as an example. Even as our science advances and our hardware become increasingly more capable, our software will be perhaps the most important aspect in this realization. Some recommendations for the future are provided. Education of users is essential for proper use and interpretation of computational results in the future.

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Year:  2012        PMID： 22246296     DOI： 10.1007/s10822-012-9541-6

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  18 in total

1.  SAMPL2 challenge: prediction of solvation energies and tautomer ratios.

Authors:  A Geoffrey Skillman; Matthew T Geballe; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2010-04-28       Impact factor: 3.686

2.  A critical assessment of docking programs and scoring functions.

Authors:  Gregory L Warren; C Webster Andrews; Anna-Maria Capelli; Brian Clarke; Judith LaLonde; Millard H Lambert; Mika Lindvall; Neysa Nevins; Simon F Semus; Stefan Senger; Giovanna Tedesco; Ian D Wall; James M Woolven; Catherine E Peishoff; Martha S Head
Journal:  J Med Chem       Date:  2006-10-05       Impact factor: 7.446

3.  Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

Authors:  David L Mobley; Elise Dumont; John D Chodera; Ken A Dill
Journal:  J Phys Chem B       Date:  2007-02-10       Impact factor: 2.991

4.  Predicting absolute ligand binding free energies to a simple model site.

Authors:  David L Mobley; Alan P Graves; John D Chodera; Andrea C McReynolds; Brian K Shoichet; Ken A Dill
Journal:  J Mol Biol       Date:  2007-06-08       Impact factor: 5.469

5.  Assessment of standard force field models against high-quality ab initio potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions.

Authors:  C David Sherrill; Bobby G Sumpter; Mutasem O Sinnokrot; Michael S Marshall; Edward G Hohenstein; Ross C Walker; Ian R Gould
Journal:  J Comput Chem       Date:  2009-11-15       Impact factor: 3.376

6.  A blind challenge for computational solvation free energies: introduction and overview.

Authors:  J Peter Guthrie
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

7.  Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test.

Authors:  Graeme M Day; Timothy G Cooper; Aurora J Cruz-Cabeza; Katarzyna E Hejczyk; Herman L Ammon; Stephan X M Boerrigter; Jeffrey S Tan; Raffaele G Della Valle; Elisabetta Venuti; Jovan Jose; Shridhar R Gadre; Gautam R Desiraju; Tejender S Thakur; Bouke P van Eijck; Julio C Facelli; Victor E Bazterra; Marta B Ferraro; Detlef W M Hofmann; Marcus A Neumann; Frank J J Leusen; John Kendrick; Sarah L Price; Alston J Misquitta; Panagiotis G Karamertzanis; Gareth W A Welch; Harold A Scheraga; Yelena A Arnautova; Martin U Schmidt; Jacco van de Streek; Alexandra K Wolf; Bernd Schweizer
Journal:  Acta Crystallogr B       Date:  2009-03-16

8.  Functional group dependence of solute partitioning to various locations within a DOPC bilayer: a comparison of molecular dynamics simulations with experiment.

Authors:  Ravindra W Tejwani; Malcolm E Davis; Bradley D Anderson; Terry R Stouch
Journal:  J Pharm Sci       Date:  2011-01-06       Impact factor: 3.534

9.  An atomic and molecular view of the depth dependence of the free energies of solute transfer from water into lipid bilayers.

Authors:  Ravindra W Tejwani; Malcolm E Davis; Bradley D Anderson; Terry R Stouch
Journal:  Mol Pharm       Date:  2011-11-08       Impact factor: 4.939

10.  Molecular shape and medicinal chemistry: a perspective.

Authors:  Anthony Nicholls; Georgia B McGaughey; Robert P Sheridan; Andrew C Good; Gregory Warren; Magali Mathieu; Steven W Muchmore; Scott P Brown; J Andrew Grant; James A Haigh; Neysa Nevins; Ajay N Jain; Brian Kelley
Journal:  J Med Chem       Date:  2010-05-27       Impact factor: 7.446
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  9 in total

1.  R-group template CoMFA combines benefits of "ad hoc" and topomer alignments using 3D-QSAR for lead optimization.

Authors:  Richard D Cramer
Journal:  J Comput Aided Mol Des       Date:  2012-06-04       Impact factor: 3.686

2.  ALOHA: a novel probability fusion approach for scoring multi-parameter drug-likeness during the lead optimization stage of drug discovery.

Authors:  Derek A Debe; Ravindra B Mamidipaka; Robert J Gregg; James T Metz; Rishi R Gupta; Steven W Muchmore
Journal:  J Comput Aided Mol Des       Date:  2013-10-11       Impact factor: 3.686

Review 3.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

Review 4.  Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

Authors:  Pnina Dauber-Osguthorpe; A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

5.  Fitting and handling dose response data.

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

6.  Template CoMFA Generates Single 3D-QSAR Models that, for Twelve of Twelve Biological Targets, Predict All ChEMBL-Tabulated Affinities.

Authors:  Richard D Cramer
Journal:  PLoS One       Date:  2015-06-12       Impact factor: 3.240

Review 7.  Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery.

Authors:  Valère Lounnas; Tina Ritschel; Jan Kelder; Ross McGuire; Robert P Bywater; Nicolas Foloppe
Journal:  Comput Struct Biotechnol J       Date:  2013-04-02       Impact factor: 7.271

8.  iDrug: a web-accessible and interactive drug discovery and design platform.

Authors:  Xia Wang; Haipeng Chen; Feng Yang; Jiayu Gong; Shiliang Li; Jianfeng Pei; Xiaofeng Liu; Hualiang Jiang; Luhua Lai; Honglin Li
Journal:  J Cheminform       Date:  2014-05-23       Impact factor: 5.514

9.  CSAR data set release 2012: ligands, affinities, complexes, and docking decoys.

Authors:  James B Dunbar; Richard D Smith; Kelly L Damm-Ganamet; Aqeel Ahmed; Emilio Xavier Esposito; James Delproposto; Krishnapriya Chinnaswamy; You-Na Kang; Ginger Kubish; Jason E Gestwicki; Jeanne A Stuckey; Heather A Carlson
Journal:  J Chem Inf Model       Date:  2013-05-10       Impact factor: 4.956
  9 in total

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