Literature DB >> 16328855

Molecular shape and electrostatics in the encoding of relevant chemical information.

Anthony Nicholls1, J Andrew Grant.   

Abstract

We propose a molecule's chemistry can be hidden by representations of its shape and electrostatic field while retaining crucial, pharmaceutically relevant, information. Necessary, but not sufficient, to this proposition are the importance of shape and electrostatics to activity, the facility to easily represent, store and compare field properties, and knowledge of the density of possible drug-like molecules within a given radius of physical similarity. We provide methods and evidence to support the conclusion that a useful encoding is practical and propose tests for falsification.

Mesh:

Year:  2005        PMID: 16328855     DOI: 10.1007/s10822-005-9019-x

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


  13 in total

1.  Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.

Authors:  C Bissantz; G Folkers; D Rognan
Journal:  J Med Chem       Date:  2000-12-14       Impact factor: 7.446

2.  A novel shape-feature based approach to virtual library screening.

Authors:  Santosh Putta; Christian Lemmen; Paul Beroza; Jonathan Greene
Journal:  J Chem Inf Comput Sci       Date:  2002 Sep-Oct

3.  Reoptimization of MDL keys for use in drug discovery.

Authors:  Joseph L Durant; Burton A Leland; Douglas R Henry; James G Nourse
Journal:  J Chem Inf Comput Sci       Date:  2002 Nov-Dec

4.  Assessing the performance of OMEGA with respect to retrieving bioactive conformations.

Authors:  Jonas Boström; Jeremy R Greenwood; Johan Gottfries
Journal:  J Mol Graph Model       Date:  2003-03       Impact factor: 2.518

5.  Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding.

Authors:  Emanuele Perola; Paul S Charifson
Journal:  J Med Chem       Date:  2004-05-06       Impact factor: 7.446

6.  Virtual exploration of the small-molecule chemical universe below 160 Daltons.

Authors:  Tobias Fink; Heinz Bruggesser; Jean-Louis Reymond
Journal:  Angew Chem Int Ed Engl       Date:  2005-02-25       Impact factor: 15.336

7.  Conformational energy penalties of protein-bound ligands.

Authors:  J Boström; P O Norrby; T Liljefors
Journal:  J Comput Aided Mol Des       Date:  1998-07       Impact factor: 3.686

Review 8.  The art and practice of structure-based drug design: a molecular modeling perspective.

Authors:  R S Bohacek; C McMartin; W C Guida
Journal:  Med Res Rev       Date:  1996-01       Impact factor: 12.944

9.  Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics.

Authors:  B B Masek; A Merchant; J B Matthew
Journal:  Proteins       Date:  1993-10

10.  Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin.

Authors:  Heshu Lu; Debbie J Chang; Blandine Baratte; Laurent Meijer; Ursula Schulze-Gahmen
Journal:  J Med Chem       Date:  2005-02-10       Impact factor: 7.446

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  9 in total

1.  Enantiomeric propanolamines as selective N-methyl-D-aspartate 2B receptor antagonists.

Authors:  Yesim A Tahirovic; Matthew Geballe; Ewa Gruszecka-Kowalik; Scott J Myers; Polina Lyuboslavsky; Phuong Le; Adam French; Hasan Irier; Woo-Baeg Choi; Keith Easterling; Hongjie Yuan; Lawrence J Wilson; Robert Kotloski; James O McNamara; Raymond Dingledine; Dennis C Liotta; Stephen F Traynelis; James P Snyder
Journal:  J Med Chem       Date:  2008-09-25       Impact factor: 7.446

2.  Computation of 3D queries for ROCS based virtual screens.

Authors:  Gregory J Tawa; J Christian Baber; Christine Humblet
Journal:  J Comput Aided Mol Des       Date:  2009-09-26       Impact factor: 3.686

3.  Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015.

Authors:  Ashutosh Kumar; Kam Y J Zhang
Journal:  J Comput Aided Mol Des       Date:  2016-08-02       Impact factor: 3.686

Review 4.  Classification of scaffold-hopping approaches.

Authors:  Hongmao Sun; Gregory Tawa; Anders Wallqvist
Journal:  Drug Discov Today       Date:  2011-10-26       Impact factor: 7.851

5.  Ligand-based virtual screening approach using a new scoring function.

Authors:  Adel Hamza; Ning-Ning Wei; Chang-Guo Zhan
Journal:  J Chem Inf Model       Date:  2012-04-09       Impact factor: 4.956

6.  Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.

Authors:  Sidhartha Chaudhury; Mohamed Diwan M Abdulhameed; Narender Singh; Gregory J Tawa; Patrik M D'haeseleer; Adam T Zemla; Ali Navid; Carol E Zhou; Matthew C Franklin; Jonah Cheung; Michael J Rudolph; James Love; John F Graf; David A Rozak; Jennifer L Dankmeyer; Kei Amemiya; Simon Daefler; Anders Wallqvist
Journal:  PLoS One       Date:  2013-05-21       Impact factor: 3.240

Review 7.  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

8.  Identification of fragments targeting an alternative pocket on HIV-1 gp41 by NMR screening and similarity searching.

Authors:  Shidong Chu; Miriam Gochin
Journal:  Bioorg Med Chem Lett       Date:  2013-07-22       Impact factor: 2.823

9.  Fragment-hopping-based discovery of a novel chemical series of proto-oncogene PIM-1 kinase inhibitors.

Authors:  Gustavo Saluste; Maria I Albarran; Rosa M Alvarez; Obdulia Rabal; Miguel Angel Ortega; Carmen Blanco; Guido Kurz; Antonio Salgado; Paolo Pevarello; James R Bischoff; Joaquin Pastor; Julen Oyarzabal
Journal:  PLoS One       Date:  2012-10-24       Impact factor: 3.240

  9 in total

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