Literature DB >> 25660403

A review of methods for the calculation of solution free energies and the modelling of systems in solution.

R E Skyner1, J L McDonagh, C R Groom, T van Mourik, J B O Mitchell.   

Abstract

Over the past decade, pharmaceutical companies have seen a decline in the number of drug candidates successfully passing through clinical trials, though billions are still spent on drug development. Poor aqueous solubility leads to low bio-availability, reducing pharmaceutical effectiveness. The human cost of inefficient drug candidate testing is of great medical concern, with fewer drugs making it to the production line, slowing the development of new treatments. In biochemistry and biophysics, water mediated reactions and interactions within active sites and protein pockets are an active area of research, in which methods for modelling solvated systems are continually pushed to their limits. Here, we discuss a multitude of methods aimed towards solvent modelling and solubility prediction, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.

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Year:  2015        PMID: 25660403     DOI: 10.1039/c5cp00288e

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  40 in total

1.  Synergistic long-range effects of mutations underlie aggregation propensities of amylin analogues.

Authors:  Nelson A Alves; Luis G Dias; Rafael B Frigori
Journal:  J Mol Model       Date:  2019-08-19       Impact factor: 1.810

2.  Accurate acid dissociation constant (pKa) calculation for the sulfachloropyridazine and similar molecules.

Authors:  Fernando Marques Carvalho; Yuri Alves de Oliveira Só; Alessandra Sofia Kiametis Wernik; Mônica de Abreu Silva; Ricardo Gargano
Journal:  J Mol Model       Date:  2021-07-29       Impact factor: 1.810

3.  Evaluating electronic structure methods for accurate calculation of 19 F chemical shifts in fluorinated amino acids.

Authors:  Jayangika N Dahanayake; Chandana Kasireddy; Jonathan M Ellis; Derek Hildebrandt; Olivia A Hull; Joseph P Karnes; Dylan Morlan; Katie R Mitchell-Koch
Journal:  J Comput Chem       Date:  2017-08-21       Impact factor: 3.376

4.  Solvent effect on the degree of (a)synchronicity in polar Diels-Alder reactions from the perspective of the reaction force constant analysis.

Authors:  Diana Yepes; Jorge I Martínez-Araya; Pablo Jaque
Journal:  J Mol Model       Date:  2017-12-29       Impact factor: 1.810

5.  A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approach.

Authors:  Evrim Arslan; Basak K Findik; Viktorya Aviyente
Journal:  J Comput Aided Mol Des       Date:  2020-01-14       Impact factor: 3.686

6.  Conformational Populations of β-(1→4) O-Glycosidic Linkages Using Redundant NMR J-Couplings and Circular Statistics.

Authors:  Wenhui Zhang; Toby Turney; Reagan Meredith; Qingfeng Pan; Luke Sernau; Xiaocong Wang; Xiaosong Hu; Robert J Woods; Ian Carmichael; Anthony S Serianni
Journal:  J Phys Chem B       Date:  2017-03-30       Impact factor: 2.991

Review 7.  Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.

Authors:  Megan L Peach; Raul E Cachau; Marc C Nicklaus
Journal:  J Mol Recognit       Date:  2017-02-24       Impact factor: 2.137

8.  Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Authors:  Guilherme Duarte Ramos Matos; Daisy Y Kyu; Hannes H Loeffler; John D Chodera; Michael R Shirts; David L Mobley
Journal:  J Chem Eng Data       Date:  2017-04-24       Impact factor: 2.694

9.  Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

Authors:  John A Keith; Valentin Vassilev-Galindo; Bingqing Cheng; Stefan Chmiela; Michael Gastegger; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

10.  Determining the hydration free energies of selected small molecules with MP2 and local MP2 through adaptive force matching.

Authors:  Dong Zheng; Ying Yuan; Feng Wang
Journal:  J Chem Phys       Date:  2021-03-14       Impact factor: 3.488

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