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Literature DB >> 15272829

Topomers: a validated protocol for their self-consistent generation.

Abstract

The hypothesis underlying topomer development is that describing molecular structures consistently may be at least as productive as describing them more realistically but incompletely. A general protocol is detailed for deterministically generating self-consistent shapes of molecular fragments from their topologies. These and other extensions to the topomer methodology are validated by repetition of earlier benchmark studies.

Year: 2004 PMID： 15272829 DOI： 10.1021/ci049961d

Source DB: PubMed Journal: J Chem Inf Comput Sci ISSN： 0095-2338

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Cited

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

Authors: Richard D Cramer
Journal: J Comput Aided Mol Des Date: 2010-03-21 Impact factor: 3.686

Review 3. Pushing the boundaries of 3D-QSAR.

Authors: Richard D Cramer; Bernd Wendt
Journal: J Comput Aided Mol Des Date: 2007-01-26 Impact factor: 3.686

4. Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis.

Authors: Bernd Wendt; Richard D Cramer
Journal: J Comput Aided Mol Des Date: 2008-02-27 Impact factor: 3.686

Review 5. Computational methods in drug discovery.

Authors: Gregory Sliwoski; Sandeepkumar Kothiwale; Jens Meiler; Edward W Lowe
Journal: Pharmacol Rev Date: 2013-12-31 Impact factor: 25.468

6. QSAR modeling: where have you been? Where are you going to?

Authors: Artem Cherkasov; Eugene N Muratov; Denis Fourches; Alexandre Varnek; Igor I Baskin; Mark Cronin; John Dearden; Paola Gramatica; Yvonne C Martin; Roberto Todeschini; Viviana Consonni; Victor E Kuz'min; Richard Cramer; Romualdo Benigni; Chihae Yang; James Rathman; Lothar Terfloth; Johann Gasteiger; Ann Richard; Alexander Tropsha
Journal: J Med Chem Date: 2014-01-06 Impact factor: 7.446

Topomers: a validated protocol for their self-consistent generation.

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

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

Review 3. Pushing the boundaries of 3D-QSAR.

4. Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis.

Review 5. Computational methods in drug discovery.

6. QSAR modeling: where have you been? Where are you going to?

7. Herman Skolnik award symposium honoring Yvonne Martin.

8. Identification of novel anthrax toxin countermeasures using in silico methods.

9. 2D-SAR and 3D-QSAR analyses for acetylcholinesterase inhibitors.

10. Challenging the gold standard for 3D-QSAR: template CoMFA versus X-ray alignment.