(Q34978169)

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Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints

scientific article published on May 18, 2011

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scholarly article

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Europe PubMed Central

PubMed publication ID

5 August 2017

Accurate determination of the binding free energy for KcsA-charybdotoxin complex from the potential of mean force calculations with restraints (English)

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints (English)

1 reference

10.1016/J.BPJ.2011.03.052

https://api.crossref.org/works/10.1016/J.BPJ.2011.03.052

2 December 2024

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Po-Chia Chen

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Serdar Kuyucak

2

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publication date

1 May 2011

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Europe PubMed Central

PubMed publication ID

5 August 2017

18 May 2011

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National Center for Biotechnology Information

PubMed publication ID

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21575581

2 December 2024

full work available at URL

http://www.cell.com/article/S0006349511004103/pdf

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21575581

2 December 2024

https://europepmc.org/articles/PMC3093566

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Europe PubMed Central

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21575581

2 December 2024

https://europepmc.org/articles/PMC3093566?pdf=render

Portable Document Format

online access status

content deliverer

Europe PubMed Central

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21575581

2 December 2024

https://doi.org/10.1016/j.bpj.2011.03.052

online access status

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21575581

2 December 2024

https://api.elsevier.com/content/article/PII:S0006349511004103?httpAccept=text/xml

1 reference

10.1016/J.BPJ.2011.03.052

https://api.crossref.org/works/10.1016/J.BPJ.2011.03.052

2 December 2024

https://api.elsevier.com/content/article/PII:S0006349511004103?httpAccept=text/plain

1 reference

10.1016/J.BPJ.2011.03.052

https://api.crossref.org/works/10.1016/J.BPJ.2011.03.052

2 December 2024

Biophysical Journal

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

100

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

10

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

2466-2474

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Towards accurate free energy calculations in ligand protein-binding studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Basic ingredients of free energy calculations: a review

1 reference

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8 July 2018

Calculation of free-energy differences by confinement simulations. Application to peptide conformers

1 reference

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8 July 2018

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

1 reference

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8 July 2018

Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Computations of standard binding free energies with molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Calculation of protein-ligand binding affinities.

1 reference

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8 July 2018

Combining docking and molecular dynamic simulations in drug design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Nuclear magnetic resonance structural studies of a potassium channel-charybdotoxin complex.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Scalable molecular dynamics with NAMD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Crystal structure of a mammalian voltage-dependent Shaker family K+ channel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Calculation of absolute protein-ligand binding free energy from computer simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Contribution of the functional dyad of animal toxins acting on voltage-gated Kv1-type channels.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Potassium channel blockade by the sea anemone toxin ShK for the treatment of multiple sclerosis and other autoimmune diseases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Simulation of the interaction between ScyTx and small conductance calcium-activated potassium channel by docking and MM-PBSA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Current views on scorpion toxins specific for K+-channels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

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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8 July 2018

Structure-activity relationship for extracellular block of K+ channels by tetraalkylammonium ions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Escaping free-energy minima

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Analysis of side-chain organization on a refined model of charybdotoxin: structural and functional implications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093566

8 July 2018

Molecular basis of inhibitory peptide maurotoxin recognizing Kv1.2 channel explored by ZDOCK and molecular dynamic simulations

1 reference

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26 October 2018

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

1 reference

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26 October 2018

Binding of organic cations to gramicidin A channel studied with AutoDock and molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/21575581

12 December 2020

based on heuristic

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

32

1 reference

10.1016/J.BPJ.2011.03.052

https://api.crossref.org/works/10.1016/J.BPJ.2011.03.052

2 December 2024

Identifiers

10.1016/J.BPJ.2011.03.052

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

ResearchGate publication ID

0 references

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