(Q30582034)

English

Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations (English)

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

molecular dynamics simulation

0 references

1 reference

based on heuristic

inferred from title

Hepatitis C virus

1 reference

based on heuristic

inferred from title

Thomas E. Cheatham, III

4

object named as

Thomas E Cheatham

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

author name string

Niel M Henriksen

1

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

Hamed S Hayatshahi

2

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

Darrell R Davis

3

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

publication date

3 June 2014

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

Journal of Chemical Information and Modeling

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

54

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

6

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

1758-1772

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

describes a project that uses

molecular dynamics simulation

1 reference

based on heuristic

inferred from title

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Aminoglycoside antibiotics in the 21st century.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Novel insights of structure-based modeling for RNA-targeted drug discovery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Cations in charge: magnesium ions in RNA folding and catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Evaluation of DNA Force Fields in Implicit Solvation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Importance of diffuse metal ion binding to RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Ribozymes: Flexible molecular devices at work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Catalysis by the nucleolytic ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Therapeutic targeting of HCV internal ribosomal entry site RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Inhibitor-induced structural change in the HCV IRES domain IIa RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

DOCK 6: combining techniques to model RNA-small molecule complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

RNA folding: thermodynamic and molecular descriptions of the roles of ions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Structure and function of HCV IRES domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Extraction of configurational entropy from molecular simulations via an expansion approximation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Automatic atom type and bond type perception in molecular mechanical calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

SAR by MS: discovery of a new class of RNA-binding small molecules for the hepatitis C virus: internal ribosome entry site IIA subdomain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

The Amber biomolecular simulation programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Molecular insights into aminoglycoside action and resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

UCSF Chimera--a visualization system for exploratory research and analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Development and testing of a general amber force field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Structure of HCV IRES domain II determined by NMR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Contribution of translational and rotational motions to molecular association in aqueous solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

RNA as a target for small molecules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

The statistical-thermodynamic basis for computation of binding affinities: a critical review

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

20 June 2018

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

26 November 2018

The influence of monovalent cation size on the stability of RNA tertiary structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

26 November 2018

Implicit nonpolar solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

26 November 2018

Functional architecture of HCV IRES domain II stabilized by divalent metal ions in the crystal and in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

26 November 2018

How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

26 November 2018

Contributions to the binding free energy of ligands to avidin and streptavidin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

26 November 2018

ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4076022

26 November 2018

Ligand binding affinity prediction by linear interaction energy methods

1 reference

https://pubmed.ncbi.nlm.nih.gov/24835734

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Estimation of the ionization pK(a) of pharmaceutical substances using the computer program Sparc

1 reference

https://pubmed.ncbi.nlm.nih.gov/24835734

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stabilization of RNA tertiary structure by monovalent cations

1 reference

https://pubmed.ncbi.nlm.nih.gov/24835734

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/CI500132C

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

DBLP publication ID

journals/jcisd/HenriksenHDC14

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

2 October 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q30582034&oldid=1647421751"