Literature DB >> 24002455

Automated molecule editing in molecular design.

Peter W Kenny1, Carlos A Montanari, Igor M Prokopczyk, Fernanda A Sala, Geraldo Rodrigues Sartori.   

Abstract

The ability to modify chemical structures in an automated and controlled manner is useful in molecular design. This Perspective introduces the MUDO molecule editor and shows how automated molecule editing can be used to standardize structures, enumerate tautomeric and ionization states, identify matched molecular pairs. Unlike its predecessor Leatherface, MUDO can also process 3D structures and this capability can be used to link non-covalently docked ligands to proteins.

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Year:  2013        PMID： 24002455     DOI： 10.1007/s10822-013-9676-0

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


  36 in total

1.  A MATHEMATICAL CONTRIBUTION TO STRUCTURE-ACTIVITY STUDIES.

Authors:  S M FREE; J W WILSON
Journal:  J Med Chem       Date:  1964-07       Impact factor: 7.446

2.  Matched molecular pairs as a medicinal chemistry tool.

Authors:  Ed Griffen; Andrew G Leach; Graeme R Robb; Daniel J Warner
Journal:  J Med Chem       Date:  2011-09-22       Impact factor: 7.446

3.  Relating molecular properties and in vitro assay results to in vivo drug disposition and toxicity outcomes.

Authors:  Jeffrey J Sutherland; John W Raymond; James L Stevens; Thomas K Baker; David E Watson
Journal:  J Med Chem       Date:  2012-07-05       Impact factor: 7.446

4.  Activity landscape representations for structure-activity relationship analysis.

Authors:  Anne Mai Wassermann; Mathias Wawer; Jürgen Bajorath
Journal:  J Med Chem       Date:  2010-09-16       Impact factor: 7.446

5.  Lead optimization using matched molecular pairs: inclusion of contextual information for enhanced prediction of HERG inhibition, solubility, and lipophilicity.

Authors:  George Papadatos; Muhammad Alkarouri; Valerie J Gillet; Peter Willett; Visakan Kadirkamanathan; Christopher N Luscombe; Gianpaolo Bravi; Nicola J Richmond; Stephen D Pickett; Jameed Hussain; John M Pritchard; Anthony W J Cooper; Simon J F Macdonald
Journal:  J Chem Inf Model       Date:  2010-10-25       Impact factor: 4.956

6.  ZINC--a free database of commercially available compounds for virtual screening.

Authors:  John J Irwin; Brian K Shoichet
Journal:  J Chem Inf Model       Date:  2005 Jan-Feb       Impact factor: 4.956

7.  Statistical tools for virtual screening.

Authors:  Jennifer R Krumrine; Andrew T Maynard; Charles L Lerman
Journal:  J Med Chem       Date:  2005-11-17       Impact factor: 7.446

8.  On outliers and activity cliffs--why QSAR often disappoints.

Authors:  Gerald M Maggiora
Journal:  J Chem Inf Model       Date:  2006 Jul-Aug       Impact factor: 4.956

Review 9.  Matched molecular pair analysis in drug discovery.

Authors:  Alexander G Dossetter; Edward J Griffen; Andrew G Leach
Journal:  Drug Discov Today       Date:  2013-04-02       Impact factor: 7.851

10.  So you think you understand tautomerism?

Authors:  Roger A Sayle
Journal:  J Comput Aided Mol Des       Date:  2010-03-23       Impact factor: 3.686
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  3 in total

1.  The influence of hydrogen bonding on partition coefficients.

Authors:  Nádia Melo Borges; Peter W Kenny; Carlos A Montanari; Igor M Prokopczyk; Jean F R Ribeiro; Josmar R Rocha; Geraldo Rodrigues Sartori
Journal:  J Comput Aided Mol Des       Date:  2017-01-04       Impact factor: 3.686

2.  Ligand efficiency metrics considered harmful.

Authors:  Peter W Kenny; Andrei Leitão; Carlos A Montanari
Journal:  J Comput Aided Mol Des       Date:  2014-06-05       Impact factor: 3.686

3.  Molecular Design, Synthesis and Trypanocidal Activity of Dipeptidyl Nitriles as Cruzain Inhibitors.

Authors:  Leandro A A Avelar; Cristian D Camilo; Sérgio de Albuquerque; William B Fernandes; Cristiana Gonçalez; Peter W Kenny; Andrei Leitão; James H McKerrow; Carlos A Montanari; Erika V Meñaca Orozco; Jean F R Ribeiro; Josmar R Rocha; Fabiana Rosini; Marta E Saidel
Journal:  PLoS Negl Trop Dis       Date:  2015-07-14
  3 in total

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