Literature DB >> 23747334

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.

Jiří Šponer1, Judit E Šponer, Arnošt Mládek, Pavel Banáš, Petr Jurečka, Michal Otyepka.   

Abstract

In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments.
Copyright © 2013 Elsevier Inc. All rights reserved.

Keywords:  DNA structure; Molecular mechanics; Molecular structures and energies; Quantum chemistry

Mesh:

Substances:

Year:  2013        PMID: 23747334     DOI: 10.1016/j.ymeth.2013.05.025

Source DB:  PubMed          Journal:  Methods        ISSN: 1046-2023            Impact factor:   3.608


  12 in total

1.  Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.

Authors:  Nicholas M Gravina; James C Gumbart; Harold D Kim
Journal:  J Phys Chem B       Date:  2021-04-19       Impact factor: 2.991

2.  Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution.

Authors:  Dominic Wagner; Jörg Rinnenthal; Franz Narberhaus; Harald Schwalbe
Journal:  Nucleic Acids Res       Date:  2015-05-04       Impact factor: 16.971

3.  How Does Mg2+ Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair.

Authors:  Antarip Halder; Rohit Roy; Dhananjay Bhattacharyya; Abhijit Mitra
Journal:  Biophys J       Date:  2017-05-12       Impact factor: 4.033

Review 4.  Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.

Authors:  Daniel L Kellerman; Darrin M York; Joseph A Piccirilli; Michael E Harris
Journal:  Curr Opin Chem Biol       Date:  2014-07-12       Impact factor: 8.822

Review 5.  RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors:  Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal:  Chem Rev       Date:  2018-01-03       Impact factor: 60.622

6.  Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment.

Authors:  Reid F Brown; Casey T Andrews; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2015-04-07       Impact factor: 6.006

7.  2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes.

Authors:  Elzbieta Sochacka; Roman H Szczepanowski; Marek Cypryk; Milena Sobczak; Magdalena Janicka; Karina Kraszewska; Paulina Bartos; Anna Chwialkowska; Barbara Nawrot
Journal:  Nucleic Acids Res       Date:  2015-02-17       Impact factor: 16.971

8.  Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.

Authors:  Julien C Thibault; Daniel R Roe; Julio C Facelli; Thomas E Cheatham
Journal:  J Cheminform       Date:  2014-01-30       Impact factor: 5.514

9.  Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure.

Authors:  Valentina D'Atri; Massimiliano Porrini; Frédéric Rosu; Valérie Gabelica
Journal:  J Mass Spectrom       Date:  2015-05       Impact factor: 1.982

10.  iBIOMES Lite: summarizing biomolecular simulation data in limited settings.

Authors:  Julien C Thibault; Thomas E Cheatham; Julio C Facelli
Journal:  J Chem Inf Model       Date:  2014-06-09       Impact factor: 4.956

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.