Literature DB >> 20306282

Tautomers and topomers: challenging the uncertainties of direct physicochemical modeling.

Richard D Cramer1.   

Abstract

To address the goal of improved discovery decision making, the uncertainties of physicochemical modeling, as exemplified by tautomer identification, are contrasted with methods focused exclusively on the sole experimental system variable, the changes in ligand structures, as exemplified by topomers.

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Year:  2010        PMID： 20306282     DOI： 10.1007/s10822-010-9330-z

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


  20 in total

1.  Prospective identification of biologically active structures by topomer shape similarity searching.

Authors:  R D Cramer; M A Poss; M A Hermsmeier; T J Caulfield; M C Kowala; M T Valentine
Journal:  J Med Chem       Date:  1999-09-23       Impact factor: 7.446

Review 2.  Structure-based virtual screening: an overview.

Authors:  Paul D Lyne
Journal:  Drug Discov Today       Date:  2002-10-15       Impact factor: 7.851

3.  Do structurally similar molecules have similar biological activity?

Authors:  Yvonne C Martin; James L Kofron; Linda M Traphagen
Journal:  J Med Chem       Date:  2002-09-12       Impact factor: 7.446

4.  "Lead hopping". Validation of topomer similarity as a superior predictor of similar biological activities.

Authors:  Richard D Cramer; Robert J Jilek; Stefan Guessregen; Stephanie J Clark; Bernd Wendt; Robert D Clark
Journal:  J Med Chem       Date:  2004-12-30       Impact factor: 7.446

5.  3D-QSAR illusions.

Authors:  Arthur M Doweyko
Journal:  J Comput Aided Mol Des       Date:  2004 Jul-Sep       Impact factor: 3.686

6.  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

7.  Virtual screening for R-groups, including predicted pIC50 contributions, within large structural databases, using Topomer CoMFA.

Authors:  Richard D Cramer; Phillip Cruz; Gunther Stahl; William C Curtiss; Brian Campbell; Brian B Masek; Farhad Soltanshahi
Journal:  J Chem Inf Model       Date:  2008-11       Impact factor: 4.956

8.  Bioisosterism as a molecular diversity descriptor: steric fields of single "topomeric" conformers.

Authors:  R D Cramer; R D Clark; D E Patterson; A M Ferguson
Journal:  J Med Chem       Date:  1996-08-02       Impact factor: 7.446

9.  Substructural analysis. A novel approach to the problem of drug design.

Authors:  R D Cramer; G Redl; C E Berkoff
Journal:  J Med Chem       Date:  1974-05       Impact factor: 7.446

10.  What anions do inside a receptor's cavity: a trifurcate anion receptor providing both electrostatic and hydrogen-bonding interactions.

Authors:  Valeria Amendola; Massimo Boiocchi; Luigi Fabbrizzi; Arianna Palchetti
Journal:  Chemistry       Date:  2005-09-19       Impact factor: 5.236
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  3 in total

1.  pK(a) based protonation states and microspecies for protein-ligand docking.

Authors:  Tim ten Brink; Thomas E Exner
Journal:  J Comput Aided Mol Des       Date:  2010-09-30       Impact factor: 3.686

2.  Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design.

Authors:  Robert D Clark; Marvin Waldman
Journal:  J Comput Aided Mol Des       Date:  2011-12-10       Impact factor: 3.686

3.  Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration.

Authors:  Nathaniel W Silver; Bracken M King; Madhavi N L Nalam; Hong Cao; Akbar Ali; G S Kiran Kumar Reddy; Tariq M Rana; Celia A Schiffer; Bruce Tidor
Journal:  J Chem Theory Comput       Date:  2013-08-07       Impact factor: 6.006
  3 in total

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