Calculation of absolute protein-ligand binding free energy from computer simulations (Q33784404)

29 July 2017

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

1 reference

29 July 2017

1 reference

1 reference

Hyung-June Woo

1

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PubMed ID

15867154

29 July 2017

Benoît Roux

series ordinal

2

1 reference

PubMed ID

15867154

29 July 2017

language of work or name

English

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publication date

2 May 2005

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Proceedings of the National Academy of Sciences of the United States of America

29 July 2017

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29 July 2017

102

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29 July 2017

6825-6830

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29 July 2017

19

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

29 July 2017

1 reference

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4 July 2018

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Free energy calculations and ligand binding

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

An investigation of phosphopeptide binding to SH2 domain

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Molecular recognition by SH2 domains

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

On the calculation of absolute macromolecular binding free energies

4 July 2018

1 reference

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Rational approach to AIDS drug design through structural biology

4 July 2018

1 reference

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Virtual screening and fast automated docking methods.

4 July 2018

1 reference

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Recognition of specific DNA sequences.

4 July 2018

1 reference

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Design of RNA-binding proteins and ligands

4 July 2018

1 reference

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Accommodating protein flexibility in computational drug design

4 July 2018

1 reference

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Energetic dissection of specificity in serine proteases

4 July 2018

1 reference

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The statistical-thermodynamic basis for computation of binding affinities: a critical review

4 July 2018

1 reference

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Reduced surface: an efficient way to compute molecular surfaces

4 July 2018

1 reference

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Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study

4 July 2018

1 reference

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Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: crystal structures of the complexed and peptide-free forms

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

SH2 domains recognize specific phosphopeptide sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

SH2 and SH3 domains: from structure to function

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Conformationally constrained peptide analogues of pTyr-Glu-Glu-Ile as inhibitors of the Src SH2 domain binding

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

30 October 2018

1 reference

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Investigation of phosphotyrosine recognition by the SH2 domain of the Src kinase

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1100764

Prediction and analysis of SH2 domain-phosphopeptide interactions

30 October 2018

1 reference

12 December 2020

Determination of affinities for lck SH2 binding peptides using a sensitive fluorescence assay: comparison between the pYEEIP and pYQPQP consensus sequences reveals context-dependent binding specificity

1 reference

12 December 2020

Calorimetric investigation of proton linkage by monitoring both the enthalpy and association constant of binding: application to the interaction of the Src SH2 domain with a high-affinity tyrosyl phosphopeptide

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0409005102

1 reference

29 July 2017

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1 reference

29 July 2017

1 reference

PubMed ID

15867154