(Q30375636)

English

Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations.

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. (English)

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

molecular dynamics simulation

0 references

J. Andrew McCammon

5

object named as

J Andrew McCammon

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

object named as

Ivaylo Ivanov

3

0 references

author name string

Rommie E Amaro

1

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Xiaolin Cheng

2

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Dong Xu

4

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

language of work or name

0 references

publication date

1 April 2009

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Journal of the American Chemical Society

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

131

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

13

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

4702-4709

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.

1 reference

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20 June 2018

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.

1 reference

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20 June 2018

Antiviral agents active against influenza A viruses.

1 reference

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20 June 2018

Comparison of multiple Amber force fields and development of improved protein backbone parameters

1 reference

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20 June 2018

The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design.

1 reference

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20 June 2018

A computational study of nucleosomal DNA flexibility

1 reference

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20 June 2018

Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity

1 reference

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Avian flu: isolation of drug-resistant H5N1 virus.

1 reference

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20 June 2018

The GROMOS software for biomolecular simulation: GROMOS05.

1 reference

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20 June 2018

The Amber biomolecular simulation programs

1 reference

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PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

1 reference

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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=2665887

20 June 2018

Exploring protein native states and large-scale conformational changes with a modified generalized born model

1 reference

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20 June 2018

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

1 reference

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Neuraminidase sequence analysis and susceptibilities of influenza virus clinical isolates to zanamivir and oseltamivir.

1 reference

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20 June 2018

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

1 reference

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Computational mapping identifies the binding sites of organic solvents on proteins

1 reference

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20 June 2018

Comparison of the activities of zanamivir, oseltamivir, and RWJ-270201 against clinical isolates of influenza virus and neuraminidase inhibitor-resistant variants

1 reference

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Comparison of efficacies of RWJ-270201, zanamivir, and oseltamivir against H5N1, H9N2, and other avian influenza viruses

1 reference

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Selection of influenza virus mutants in experimentally infected volunteers treated with oseltamivir

1 reference

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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

1 reference

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Generalized born models of macromolecular solvation effects

1 reference

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20 June 2018

BCX-1812 (RWJ-270201): discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design

1 reference

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20 June 2018

Rational design of potent sialidase-based inhibitors of influenza virus replication

1 reference

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Improved sensitivity of profile searches through the use of sequence weights and gap excision.

1 reference

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20 June 2018

Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 A resolution

1 reference

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20 June 2018

Three-dimensional structure of neuraminidase of subtype N9 from an avian influenza virus.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2665887

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Activity of the neuraminidase inhibitor A-315675 against oseltamivir-resistant influenza neuraminidases of N1 and N2 subtypes

1 reference

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Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design.

1 reference

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Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.

1 reference

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Optimal charges in lead progression: a structure-based neuraminidase case study.

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Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations

1 reference

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Identification of substrate binding sites in enzymes by computational solvent mapping.

1 reference

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Influenza virus carrying neuraminidase with reduced sensitivity to oseltamivir carboxylate has altered properties in vitro and is compromised for infectivity and replicative ability in vivo

1 reference

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Reversible peptide folding in solution by molecular dynamics simulation

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A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

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Theory and applications of the generalized Born solvation model in macromolecular simulations

1 reference

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Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: Application to Influenza neuraminidase

1 reference

https://pubmed.ncbi.nlm.nih.gov/19296611

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations.

1 reference

https://pubmed.ncbi.nlm.nih.gov/19296611

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based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/19296611

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JA8085643

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

ResearchGate publication ID

0 references

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