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Literature DB >> 31854986

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions".

Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiří Šponer, Pavel Banáš.

Abstract

Entities: Chemical Disease Gene

Year: 2019 PMID： 31854986 PMCID： PMC7495409 DOI： 10.1021/acs.jctc.9b01189

Source DB: PubMed Journal: J Chem Theory Comput ISSN： 1549-9618 Impact factor: 6.006

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11 in total

1. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations.

Authors: Petra Kührová; Michal Otyepka; Jiří Šponer; Pavel Banáš
Journal: J Chem Theory Comput Date: 2014-01-14 Impact factor: 6.006

2. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Authors: Alberto Pérez; Iván Marchán; Daniel Svozil; Jiri Sponer; Thomas E Cheatham; Charles A Laughton; Modesto Orozco
Journal: Biophys J Date: 2007-03-09 Impact factor: 4.033

3. Fitting Corrections to an RNA Force Field Using Experimental Data.

Authors: Andrea Cesari; Sandro Bottaro; Kresten Lindorff-Larsen; Pavel Banáš; Jiří Šponer; Giovanni Bussi
Journal: J Chem Theory Comput Date: 2019-05-23 Impact factor: 6.006

4. Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

Authors: Petra Kührová; Vojtěch Mlýnský; Marie Zgarbová; Miroslav Krepl; Giovanni Bussi; Robert B Best; Michal Otyepka; Jiří Šponer; Pavel Banáš
Journal: J Chem Theory Comput Date: 2019-04-02 Impact factor: 6.006

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. Water dispersion interactions strongly influence simulated structural properties of disordered protein states.

Authors: Stefano Piana; Alexander G Donchev; Paul Robustelli; David E Shaw
Journal: J Phys Chem B Date: 2015-04-13 Impact factor: 2.991

7. All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors: A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal: J Phys Chem B Date: 1998-04-30 Impact factor: 2.991

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions".

1. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations.

2. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

3. Fitting Corrections to an RNA Force Field Using Experimental Data.

4. Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

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

6. Water dispersion interactions strongly influence simulated structural properties of disordered protein states.

7. All-atom empirical potential for molecular modeling and dynamics studies of proteins.

8. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.

9. High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.

10. RNA force field with accuracy comparable to state-of-the-art protein force fields.

1. A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA.

2. Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field.

3. Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.