BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations (Q36335374)

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English	BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations	scientific article

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9 March 2020

BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations (English)

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9 March 2020

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Huan-Xiang Zhou

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9 March 2020

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Nicholas Greives

1

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9 March 2020

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1 October 2012

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9 March 2020

Journal of Chemical Physics

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9 March 2020

137

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9 March 2020

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9 March 2020

135105

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9 March 2020

Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477184

30 September 2017

Diffusion-influenced ligand binding to buried sites in macromolecules and transmembrane channels

1 reference

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30 September 2017

Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins

1 reference

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30 September 2017

Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477184

30 September 2017

From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions

1 reference

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Ligand-specific conformation of extracellular loop-2 in the angiotensin II type 1 receptor

1 reference

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Role of secondary sialic acid binding sites in influenza N1 neuraminidase

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The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design.

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A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles

1 reference

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30 September 2017

Anatomy of a proficient enzyme: The structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog

1 reference

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Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus

1 reference

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30 September 2017

Conformation gating as a mechanism for enzyme specificity

1 reference

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30 September 2017

Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions

1 reference

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30 September 2017

Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase

1 reference

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30 September 2017

Diffusion-controlled bimolecular reaction rates. The effect of rotational diffusion and orientation constraints

1 reference

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30 September 2017

Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

1 reference

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Gating and Intermolecular Interactions in Ligand-Protein Association: Coarse-Grained Modeling of HIV-1 Protease.

1 reference

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22 September 2018

Simulation of enzyme–substrate encounter with gated active sites

1 reference

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21 January 2018

Diffusive reaction rates from Brownian dynamics simulations: Replacing the outer cutoff surface by an analytical treatment

1 reference

https://api.crossref.org/works/10.1063%2F1.4756913

21 January 2018

Kinetics of diffusion-influenced reactions studied by Brownian dynamics

1 reference

https://api.crossref.org/works/10.1063%2F1.4756913

21 January 2018

A 240-Fold Electrostatic Rate-Enhancement for Acetylcholinesterase−Substrate Binding Can Be Predicted by the Potential within the Active Site

1 reference

https://api.crossref.org/works/10.1063%2F1.4756913

21 January 2018

On the calculation of diffusive reaction rates using Brownian dynamics simulations

1 reference

https://api.crossref.org/works/10.1063%2F1.4756913

21 January 2018

Theory of the diffusion-influenced substrate binding rate to a buried and gated active site

1 reference

https://api.crossref.org/works/10.1063%2F1.4756913

21 January 2018

Identifiers

10.1063/1.4756913

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23039617%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23039617%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23039617%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

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