Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease. (Q44238646)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

title

Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

David J D Wilson

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

author name string

Robert T C Brownlee

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

publication date

23 August 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computational Chemistry

11 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

volume

33

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

issue

32

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

page(s)

2566-2580

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

Domain communication in the dynamical structure of human immunodeficiency virus 1 protease

11 February 2020

cites work

1 reference

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

21 January 2018

1 reference

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state

21 January 2018

1 reference

The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts

21 January 2018

1 reference

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs

21 January 2018

1 reference

Structure, dynamics and solvation of HIV-1 protease/saquinavir complex in aqueous solution and their contributions to drug resistance: molecular dynamic simulations

21 January 2018

1 reference

Inhibitors of HIV-1 protease: a major success of structure-assisted drug design

21 January 2018

1 reference

Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir

21 January 2018

1 reference

An ethylenamine inhibitor binds tightly to both wild type and mutant HIV-1 proteases. Structure and energy study

21 January 2018

1 reference

Inhibition and substrate recognition--a computational approach applied to HIV protease

21 January 2018

1 reference

Molecular Dynamics Simulations of HIV-1 Protease Suggest Different Mechanisms Contributing to Drug Resistance.

21 January 2018

1 reference

Molecular mechanics analysis of drug-resistant mutants of HIV protease.

21 January 2018

1 reference

Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations

21 January 2018

1 reference

Cyclic HIV-1 protease inhibitors derived from mannitol: synthesis, inhibitory potencies, and computational predictions of binding affinities.

21 January 2018

1 reference

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations.

21 January 2018

1 reference

Efficient evaluation of binding free energy using continuum electrostatics solvation

21 January 2018

1 reference

Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations

21 January 2018

1 reference

Molecular mechanisms of resistance: free energy calculations of mutation effects on inhibitor binding to HIV-1 protease

21 January 2018

1 reference

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

21 January 2018

1 reference

Structure-based phenotyping predicts HIV-1 protease inhibitor resistance

21 January 2018

1 reference

Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance

21 January 2018

1 reference

Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants

21 January 2018

1 reference

Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations.

21 January 2018

1 reference

Resistant mechanism against nelfinavir of human immunodeficiency virus type 1 proteases

21 January 2018

1 reference

Computational characterization of structural role of the non-active site mutation M36I of human immunodeficiency virus type 1 protease

21 January 2018

1 reference

Insights into saquinavir resistance in the G48V HIV-1 protease: quantum calculations and molecular dynamic simulations

21 January 2018

1 reference

Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding

21 January 2018

1 reference

Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.

21 January 2018

1 reference

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

21 January 2018

1 reference

Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

21 January 2018

1 reference

Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA.

21 January 2018

1 reference

Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

21 January 2018

1 reference

Evaluating the potency of HIV-1 protease drugs to combat resistance

21 January 2018

1 reference

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

21 January 2018

1 reference

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

21 January 2018

1 reference

Assessment of free energy predictors for ligand binding to a methyllysine histone code reader

21 January 2018

1 reference

Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases

21 January 2018

1 reference

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin

21 January 2018

1 reference

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

21 January 2018

1 reference

Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?

21 January 2018

1 reference

Ligand configurational entropy and protein binding

21 January 2018

1 reference

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

21 January 2018

1 reference

MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface

21 January 2018

1 reference

BindingDB: a web-accessible molecular recognition database

21 January 2018

1 reference

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

21 January 2018

1 reference

Inhomogeneous Electron Gas

21 January 2018

1 reference

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

21 January 2018

1 reference

Density-functional exchange-energy approximation with correct asymptotic behavior

21 January 2018

1 reference

Self‐Consistent Molecular‐Orbital Methods. I. Use of Gaussian Expansions of Slater‐Type Atomic Orbitals

21 January 2018

1 reference

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

21 January 2018

1 reference

Development and testing of a general amber force field

21 January 2018

1 reference

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

21 January 2018

1 reference

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics

21 January 2018

1 reference

VMD: visual molecular dynamics

21 January 2018

1 reference

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

21 January 2018

1 reference

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

21 January 2018

1 reference

Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.

21 January 2018

1 reference

Free energy decomposition of protein-protein interactions.

21 January 2018

1 reference

Theory of biomolecular recognition

21 January 2018

1 reference

Interpreting trends in the binding of cyclic ureas to HIV-1 protease.

21 January 2018

1 reference

The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level

21 January 2018

1 reference

Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/JCC.23095

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22915442%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

DBLP publication ID

journals/jcc/OehmeBW12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference