(Q30835329)

English

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

27 June 2017

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. (English)

1 reference

Europe PubMed Central

27 June 2017

object named as

Youyong Li

2

0 references

5

object named as

Tingjun Hou

1 reference

Europe PubMed Central

27 June 2017

1

object named as

Huiyong Sun

1 reference

Europe PubMed Central

27 June 2017

author name string

Sheng Tian

3

1 reference

Europe PubMed Central

27 June 2017

Lei Xu

4

1 reference

Europe PubMed Central

27 June 2017

language of work or name

0 references

publication date

1 August 2014

1 reference

Europe PubMed Central

27 June 2017

number of pages

11

1 reference

based on heuristic

inferred from page(s)

Physical Chemistry Chemical Physics

1 reference

Europe PubMed Central

27 June 2017

16

1 reference

Europe PubMed Central

27 June 2017

31

1 reference

Europe PubMed Central

27 June 2017

16719-16729

1 reference

Europe PubMed Central

27 June 2017

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Predicting drug resistance of the HIV-1 protease using molecular interaction energy components

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Prediction of peptides binding to the PKA RIIalpha subunit using a hierarchical strategy

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Mapping the binding site of a large set of quinazoline type EGF-R inhibitors using molecular field analyses and molecular docking studies

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Computational alanine scanning of the 1:1 human growth hormone-receptor complex

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Molecular basis of the interaction for an essential subunit PA-PB1 in influenza virus RNA polymerase: insights from molecular dynamics simulation and free energy calculation

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Assessing protein kinase selectivity with molecular dynamics and mm-pbsa binding free energy calculations.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Molecular dynamics simulation, free energy calculation and structure-based 3D-QSAR studies of B-RAF kinase inhibitors.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Understanding the molecular basis of MK2-p38α signaling complex assembly: insights into protein-protein interaction by molecular dynamics and free energy studies.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Exploring the molecular basis of dsRNA recognition by Mss116p using molecular dynamics simulations and free-energy calculations.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Molecular dynamic investigations of the mutational effects on structural characteristics and tunnel geometry in CYP17A1.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Free energy via molecular simulation: applications to chemical and biomolecular systems

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Insight into crizotinib resistance mechanisms caused by three mutations in ALK tyrosine kinase using free energy calculation approaches.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Structural and energetic analyses of SNPs in drug targets and implications for drug therapy.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Pairwise solute descreening of solute charges from a dielectric medium

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Aqueous Solvation Free Energies of Ions and Ion−Water Clusters Based on an Accurate Value for the Absolute Aqueous Solvation Free Energy of the Proton

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

MM/GBSA binding energy prediction on the PDBbind data set: successes, failures, and directions for further improvement.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The PDBbind database: methodologies and updates

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Comparative assessment of scoring functions on a diverse test set.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The experimental uncertainty of heterogeneous public K(i) data.

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Automatic atom type and bond type perception in molecular mechanical calculations

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The implementation of a fast and accurate QM/MM potential method in Amber

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Development and testing of a general amber force field

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The ASTRAL Compendium in 2004

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The impact of structural genomics: expectations and outcomes

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Compensating enthalpic and entropic changes hinder binding affinity optimization

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Discovery of a Potential Allosteric Ligand Binding Site in CDK2

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Structure based drug design of crizotinib (PF-02341066), a potent and selective dual inhibitor of mesenchymal-epithelial transition factor (c-MET) kinase and anaplastic lymphoma kinase (ALK)

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Understanding microscopic binding of macrophage migration inhibitory factor with phenolic hydrazones by molecular docking, molecular dynamics simulations and free energy calculations

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

1 reference

https://api.crossref.org/works/10.1039%2FC4CP01388C

21 January 2018

Identifiers

10.1039/C4CP01388C

1 reference

Europe PubMed Central

27 June 2017

1 reference

Europe PubMed Central

27 June 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=Q30835329&oldid=1958588715"