Literature DB >> 30916997

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.

Zhifeng Jing1, Chengwen Liu1, Sara Y Cheng1, Rui Qi1, Brandon D Walker1, Jean-Philip Piquemal1,2,3, Pengyu Ren1.   

Abstract

Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.

Entities:  

Keywords:  QM/MM; molecular dynamics simulation; nucleic acid; polarizable force field; protein

Year:  2019        PMID: 30916997      PMCID: PMC6520134          DOI: 10.1146/annurev-biophys-070317-033349

Source DB:  PubMed          Journal:  Annu Rev Biophys        ISSN: 1936-122X            Impact factor:   12.981


  53 in total

1.  AMOEBA+ Classical Potential for Modeling Molecular Interactions.

Authors:  Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2019-06-11       Impact factor: 6.006

2.  Computational and Experimental Studies of Inhibitor Design for Aldolase A.

Authors:  Rui Qi; Brandon Walker; Zhifeng Jing; Maiya Yu; Gabriel Stancu; Ramakrishna Edupuganti; Kevin N Dalby; Pengyu Ren
Journal:  J Phys Chem B       Date:  2019-07-03       Impact factor: 2.991

3.  Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.

Authors:  Zhifeng Jing; Rui Qi; Marc Thibonnier; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2019-10-09       Impact factor: 6.006

4.  Cationic Dendrimers for siRNA Delivery: Computational Approaches for Characterization.

Authors:  Domenico Marson; Suzana Aulic; Maurizio Fermeglia; Erik Laurini; Sabrina Pricl
Journal:  Methods Mol Biol       Date:  2021

5.  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

6.  A Many-Body, Fully Polarizable Approach to QM/MM Simulations.

Authors:  Eleftherios Lambros; Filippo Lipparini; Gerardo Andrés Cisneros; Francesco Paesani
Journal:  J Chem Theory Comput       Date:  2020-11-19       Impact factor: 6.006

7.  A fast and high-quality charge model for the next generation general AMBER force field.

Authors:  Xibing He; Viet H Man; Wei Yang; Tai-Sung Lee; Junmei Wang
Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

8.  Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives.

Authors:  Poonam Pandey; Asaminew H Aytenfisu; Alexander D MacKerell; Sairam S Mallajosyula
Journal:  J Chem Theory Comput       Date:  2019-08-29       Impact factor: 6.006

9.  Impact of electronic polarizability on protein-functional group interactions.

Authors:  Himanshu Goel; Wenbo Yu; Vincent D Ustach; Asaminew H Aytenfisu; Delin Sun; Alexander D MacKerell
Journal:  Phys Chem Chem Phys       Date:  2020-04-06       Impact factor: 3.676

Review 10.  Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.

Authors:  Sergio Decherchi; Andrea Cavalli
Journal:  Chem Rev       Date:  2020-10-02       Impact factor: 60.622

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