Literature DB >> 17826685

The role of quantum mechanics in structure-based drug design.

Kaushik Raha1, Martin B Peters, Bing Wang, Ning Yu, Andrew M Wollacott, Lance M Westerhoff, Kenneth M Merz.   

Abstract

Herein we will focus on the use of quantum mechanics (QM) in drug design (DD) to solve disparate problems from scoring protein-ligand poses to building QM QSAR models. Through the variational principle of QM we know that we can obtain a more accurate representation of molecular systems than classical models, and while this is not a matter of debate, it still has not been shown that the expense of QM approaches is offset by improved accuracy in DD applications. Objectively validating the improved applicability and performance of QM over classical-based models in DD will be the focus of research in the coming years along with research on the conformational sampling problem as it relates to protein-ligand complexes.

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Year:  2007        PMID: 17826685     DOI: 10.1016/j.drudis.2007.07.006

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  45 in total

1.  Computational alanine scanning with linear scaling semiempirical quantum mechanical methods.

Authors:  David J Diller; Christine Humblet; Xiaohua Zhang; Lance M Westerhoff
Journal:  Proteins       Date:  2010-08-01

Review 2.  Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition.

Authors:  A A Moya-García; A Pino-Angeles; R Gil-Redondo; A Morreale; F Sánchez-Jiménez
Journal:  Br J Pharmacol       Date:  2009-05       Impact factor: 8.739

Review 3.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

4.  Further analysis and comparative study of intermolecular interactions using dimers from the S22 database.

Authors:  Laszlo Fusti Molnar; Xiao He; Bing Wang; Kenneth M Merz
Journal:  J Chem Phys       Date:  2009-08-14       Impact factor: 3.488

5.  A QM/MM study of the binding of RAPTA ligands to cathepsin B.

Authors:  Antonella Ciancetta; Samuel Genheden; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2011-06-24       Impact factor: 3.686

6.  Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.

Authors:  Petr Dobeš; Jindřich Fanfrlík; Jan Rezáč; Michal Otyepka; Pavel Hobza
Journal:  J Comput Aided Mol Des       Date:  2011-02-01       Impact factor: 3.686

Review 7.  Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.

Authors:  Anders S Christensen; Tomáš Kubař; Qiang Cui; Marcus Elstner
Journal:  Chem Rev       Date:  2016-04-13       Impact factor: 60.622

Review 8.  Software and resources for computational medicinal chemistry.

Authors:  Chenzhong Liao; Markus Sitzmann; Angelo Pugliese; Marc C Nicklaus
Journal:  Future Med Chem       Date:  2011-06       Impact factor: 3.808

9.  Reaction Pathway and Free Energy Profile for Cocaine Hydrolase-Catalyzed Hydrolysis of (-)-Cocaine.

Authors:  Junjun Liu; Chang-Guo Zhan
Journal:  J Chem Theory Comput       Date:  2012-03-06       Impact factor: 6.006

10.  Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods.

Authors:  Katarina Roos; Anders Hogner; Derek Ogg; Martin J Packer; Eva Hansson; Kenneth L Granberg; Emma Evertsson; Anneli Nordqvist
Journal:  J Comput Aided Mol Des       Date:  2015-11-16       Impact factor: 3.686

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