Literature DB >> 25414519

Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics.

Andrey V Ilatovskiy1, Ruben Abagyan2, Irina Kufareva2.   

Abstract

The rapid growth of the available crystallographic information about proteins and binding pockets creates remarkable opportunities for enriching the drug research pipelines with computational prediction of novel protein-ligand interactions. While ab initio quantum mechanical approaches are known to provide unprecedented accuracy in structure-based binding energy calculations, they are limited to only small systems of dozens of atoms. In the structural chemogenomics era, it is critical that new approaches are developed that enable application of QM methodologies to non-covalent interactions in systems as large as protein-ligand complexes and conformational ensembles. This perspective highlights recent advances towards bridging the gap between high accuracy and high volume computations in drug research.

Entities:  

Keywords:  Pocketome; Protein-ligand complex; binding energy prediction; binding pocket ensemble; virtual ligand screening

Year:  2013        PMID: 25414519      PMCID: PMC4235788          DOI: 10.1002/qua.24400

Source DB:  PubMed          Journal:  Int J Quantum Chem        ISSN: 0020-7608            Impact factor:   2.444


  74 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors:  Araz Jakalian; David B Jack; Christopher I Bayly
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

3.  Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.

Authors:  Robert Abel; Tom Young; Ramy Farid; Bruce J Berne; Richard A Friesner
Journal:  J Am Chem Soc       Date:  2008-02-12       Impact factor: 15.419

Review 4.  Covalent modifiers: an orthogonal approach to drug design.

Authors:  Michele H Potashman; Mark E Duggan
Journal:  J Med Chem       Date:  2009-03-12       Impact factor: 7.446

5.  A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets.

Authors:  Goutam Mukherjee; Niladri Patra; Poranjyoti Barua; B Jayaram
Journal:  J Comput Chem       Date:  2010-10-22       Impact factor: 3.376

6.  Combination of docking, molecular dynamics and quantum mechanical calculations for metabolism prediction of 3,4-methylenedioxybenzoyl-2-thienylhydrazone.

Authors:  Rodolpho C Braga; Vinícius M Alves; Carlos A M Fraga; Eliezer J Barreiro; Valéria de Oliveira; Carolina H Andrade
Journal:  J Mol Model       Date:  2011-09-08       Impact factor: 1.810

7.  sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins.

Authors:  Jamel Meslamani; Didier Rognan; Esther Kellenberger
Journal:  Bioinformatics       Date:  2011-03-12       Impact factor: 6.937

Review 8.  GAMESS as a free quantum-mechanical platform for drug research.

Authors:  Yuri Alexeev; Michael P Mazanetz; Osamu Ichihara; Dmitri G Fedorov
Journal:  Curr Top Med Chem       Date:  2012       Impact factor: 3.295

9.  Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450.

Authors:  Julianna Oláh; Adrian J Mulholland; Jeremy N Harvey
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-28       Impact factor: 11.205

10.  Ongoing and future developments at the Universal Protein Resource.

Authors: 
Journal:  Nucleic Acids Res       Date:  2010-11-04       Impact factor: 16.971

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  3 in total

Review 1.  Quantum mechanics implementation in drug-design workflows: does it really help?

Authors:  Olayide A Arodola; Mahmoud Es Soliman
Journal:  Drug Des Devel Ther       Date:  2017-08-31       Impact factor: 4.162

2.  Automatic generation of complementary auxiliary basis sets for explicitly correlated methods.

Authors:  Emmanouil Semidalas; Jan M L Martin
Journal:  J Comput Chem       Date:  2022-07-19       Impact factor: 3.672

3.  Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches.

Authors:  Amanda Li; Hari S Muddana; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2014-02-25       Impact factor: 6.006

  3 in total

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