(Q41921801)

English

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

scientific article published on 14 October 2010

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

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 (English)

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

3

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

1

object named as

Tingjun Hou

1 reference

Europe PubMed Central

14 October 2017

PMC publication ID

object named as

Junmei Wang

2

0 references

4

object named as

Wei Wang

1 reference

Europe PubMed Central

14 October 2017

PMC publication ID

language of work or name

1 reference

based on heuristic

inferred from title

publication date

14 October 2010

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

Journal of Computational Chemistry

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

32

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

5

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

866-877

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

Investigation of MM-PBSA rescoring of docking poses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

MM-GB/SA rescoring of docking poses in structure-based lead optimization.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 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=3043139

5 June 2018

Virtual screening of chemical libraries

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 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=3043139

5 June 2018

Recent development and application of virtual screening in drug discovery: an overview

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

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

1 reference

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5 June 2018

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

1 reference

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5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

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://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 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://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

A geometric approach to macromolecule-ligand interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

Comparative evaluation of 11 scoring functions for molecular docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 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://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

Knowledge-based scoring function to predict protein-ligand interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

A fast flexible docking method using an incremental construction algorithm.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3043139

18 August 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/20949517

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Validation and use of the MM-PBSA approach for drug discovery

1 reference

https://pubmed.ncbi.nlm.nih.gov/20949517

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase

1 reference

https://pubmed.ncbi.nlm.nih.gov/20949517

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/JCC.21666

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

DBLP publication ID

journals/jcc/HouWLW11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

ResearchGate publication ID

0 references

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