(Q37445757)

English

Docking flexible peptide to flexible protein by molecular dynamics using two implicit-solvent models: an evaluation in protein kinase and phosphatase systems

scientific article published on October 2009

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Docking flexible peptide to flexible protein by molecular dynamics using two implicit-solvent models: an evaluation in protein kinase and phosphatase systems (English)

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

author name string

Zunnan Huang

1

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Chung F Wong

2

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

language of work or name

0 references

publication date

1 October 2009

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

113

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

43

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

14343-14354

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

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Generalized Born model with a simple, robust molecular volume correction

1 reference

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Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI.

1 reference

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A mining minima approach to exploring the docking pathways of p-nitrocatechol sulfate to YopH.

1 reference

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Calculation of protein-ligand binding affinities.

1 reference

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23 August 2017

Effective handling of induced-fit motion in flexible docking.

1 reference

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Novel procedure for modeling ligand/receptor induced fit effects.

1 reference

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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

1 reference

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MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

1 reference

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High-Resolution Structure of the Yersinia pestis Protein Tyrosine Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide

1 reference

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Specificity determinants of recruitment peptides bound to phospho-CDK2/cyclin A

1 reference

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Structure and autoregulation of the insulin-like growth factor 1 receptor kinase

1 reference

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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

1 reference

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FlexE: efficient molecular docking considering protein structure variations.

1 reference

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1 reference

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1 reference

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Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm

1 reference

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Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog

1 reference

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Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine

1 reference

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Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B

1 reference

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Molecular docking to ensembles of protein structures

1 reference

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26 June 2018

Flexible protein-flexible ligand docking with disrupted velocity simulated annealing.

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2 September 2018

Prediction and scoring of docking poses with pyDock.

1 reference

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2 September 2018

FLIPDock: docking flexible ligands into flexible receptors.

1 reference

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2 September 2018

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.

1 reference

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A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors.

1 reference

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1 reference

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1 reference

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based on heuristic

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Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/19845408

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase

1 reference

https://pubmed.ncbi.nlm.nih.gov/19845408

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based on heuristic

inferred from PubMed ID database lookup

Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP907375B

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

ResearchGate publication ID

0 references

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