Literature DB >> 26821703

The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation.

Adam Pecina1, René Meier2, Jindřich Fanfrlík1, Martin Lepšík1, Jan Řezáč1, Pavel Hobza3, Carsten Baldauf4.   

Abstract

Current virtual screening tools are fast, but reliable scoring is elusive. Here, we present the 'SQM/COSMO filter', a novel scoring function featuring a quantitative semiempirical quantum mechanical (SQM) description of all types of noncovalent interactions coupled with implicit COSMO solvation. We show unequivocally that it outperforms eight widely used scoring functions. The accuracy and chemical generality of the SQM/COSMO filter make it a perfect tool for late stages of virtual screening.

Year:  2016        PMID: 26821703     DOI: 10.1039/c5cc09499b

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN: 1359-7345            Impact factor:   6.222


  7 in total

1.  On the polarization of ligands by proteins.

Authors:  Soohaeng Yoo Willow; Bing Xie; Jason Lawrence; Robert S Eisenberg; David D L Minh
Journal:  Phys Chem Chem Phys       Date:  2020-06-04       Impact factor: 3.676

2.  A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.

Authors:  Silvia Gervasoni; James Spencer; Philip Hinchliffe; Alessandro Pedretti; Franco Vairoletti; Graciela Mahler; Adrian J Mulholland
Journal:  Proteins       Date:  2021-09-20

3.  Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.

Authors:  A V Sulimov; D C Kutov; E V Katkova; V B Sulimov
Journal:  Adv Bioinformatics       Date:  2017-01-16

4.  Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms.

Authors:  Alexey V Sulimov; Dmitry A Zheltkov; Igor V Oferkin; Danil C Kutov; Ekaterina V Katkova; Eugene E Tyrtyshnikov; Vladimir B Sulimov
Journal:  Comput Struct Biotechnol J       Date:  2017-03-03       Impact factor: 7.271

5.  Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking.

Authors:  Haresh Ajani; Adam Pecina; Saltuk M Eyrilmez; Jindřich Fanfrlík; Susanta Haldar; Jan Řezáč; Pavel Hobza; Martin Lepšík
Journal:  ACS Omega       Date:  2017-07-27

6.  A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1.

Authors:  James J P Stewart
Journal:  J Mol Model       Date:  2016-10-06       Impact factor: 1.810

Review 7.  Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization.

Authors:  Claudio N Cavasotto; Natalia S Adler; Maria G Aucar
Journal:  Front Chem       Date:  2018-05-29       Impact factor: 5.221

  7 in total

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