Determination of the interfacial water content in protein-protein complexes from free energy simulations (Q41858751)

13 October 2017

Determination of the interfacial water content in protein-protein complexes from free energy simulations (English)

1 reference

13 October 2017

4

Stefan M Kast

1 reference

13 October 2017

Peter Monecke

1

1 reference

13 October 2017

Thorsten Borosch

series ordinal

2

1 reference

13 October 2017

Jürgen Brickmann

series ordinal

3

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13 October 2017

language of work or name

English

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publication date

11 November 2005

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13 October 2017

10

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inferred from page(s)

published in

Biophysical Journal

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13 October 2017

90

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13 October 2017

3

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13 October 2017

841-850

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Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

The atomic structure of protein-protein recognition sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Interactions of protein antigens with antibodies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Bound water molecules and conformational stabilization help mediate an antigen-antibody association

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Water: now you see it, now you don't

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Solvent-accessible surfaces of proteins and nucleic acids

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

A very fast program for visualizing protein surfaces, channels and cavities.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Accurate simulation of protein dynamics in solution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

The Protein Data Bank: a computer-based archival file for macromolecular structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Hybrid integral equation/simulation model for enhancing free energy computations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Grand canonical Monte Carlo simulations of water in protein environments.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

The particle concept: placing discrete water molecules during protein-ligand docking predictions.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Hydrogen bonds and salt bridges across protein-protein interfaces

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

A Strategy for the Incorporation of Water Molecules Present in a Ligand Binding Site into a Three-Dimensional Quantitative Structure−Activity Relationship Analysis

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367109

Finding and filling protein cavities using cellular logic operations

2 December 2018

1 reference

12 December 2020

Conservation of water molecules in an antibody-antigen interaction

1 reference

12 December 2020

Hydrophilicity of cavities in proteins

1 reference

12 December 2020

Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope

1 reference

12 December 2020

Hydration energy landscape of the active site cavity in cytochrome P450cam

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.065524

Identifiers

DOI

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13 October 2017

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13 October 2017

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