(Q42739070)

English

Improved estimation of ligand-macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods

scientific article published on January 2007

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

Improved estimation of ligand-macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods (English)

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

1 reference

based on heuristic

inferred from title

2

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

author name string

Akash Khandelwal

1

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

publication date

1 January 2007

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

Journal of Computer - Aided Molecular Design

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

21

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

1-3

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

131-137

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

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Modified replica exchange simulation methods for local structure refinement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

27 May 2018

Processing multimode binding situations in simulation-based prediction of ligand-macromolecule affinities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

27 May 2018

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

27 May 2018

Efficient evaluation of binding free energy using continuum electrostatics solvation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

27 May 2018

Crystal structure of human MMP9 in complex with a reverse hydroxamate inhibitor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

27 May 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=2896052

27 May 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://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

27 May 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

27 May 2018

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

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Tumour microenvironment - opinion: validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy.

1 reference

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16 August 2018

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

1 reference

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A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations

1 reference

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16 August 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

16 August 2018

Calculation of the Binding Affinity of β-Secretase Inhibitors Using the Linear Interaction Energy Method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

16 August 2018

Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside Inhibitors: Correlation of Binding Energy with Biological Activity for Novel 2-Aryl-Substituted Benzimidazole Analogues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

16 August 2018

Replica Monte Carlo simulation of spin glasses.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

16 August 2018

Calculation of relative binding free energies and configurational entropies: a structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin55-65.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2896052

16 August 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/17333483

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A new method for predicting binding affinity in computer-aided drug design

1 reference

https://pubmed.ncbi.nlm.nih.gov/17333483

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

New type of metalloproteinase inhibitor: design and synthesis of new phosphonamide-based hydroxamic acids

1 reference

https://pubmed.ncbi.nlm.nih.gov/17333483

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1007/S10822-007-9104-4

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

DBLP publication ID

journals/jcamd/KhandelwalB07

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

6 November 2017

ResearchGate publication ID

0 references

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