(Q44579014)

4 December 2017

title

Structured water molecules in the binding site of bromodomains can be displaced by cosolvent (English)

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4 December 2017

4

Amedeo Caflisch

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4 December 2017

Danzhi Huang

1

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4 December 2017

Emanuele Rossini

series ordinal

2

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4 December 2017

Sandra Steiner

series ordinal

3

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4 December 2017

publication date

26 June 2013

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4 December 2017

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4 December 2017

volume

9

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4 December 2017

issue

3

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4 December 2017

page(s)

573-579

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Bromodomain: an acetyl-lysine binding domain

4 December 2017

cites work

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

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Histone recognition and large-scale structural analysis of the human bromodomain family

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Druggability analysis and structural classification of bromodomain acetyl-lysine binding sites

21 January 2018

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Insights on HIV-1 Tat:P/CAF bromodomain molecular recognition from in vivo experiments and molecular dynamics simulations.

21 January 2018

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The role of loop ZA and Pro371 in the function of yeast Gcn5p bromodomain revealed through molecular dynamics and experiment

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The energetics of the acetylation switch in p53-mediated transcriptional activation

21 January 2018

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Functionality maps of binding sites: a multiple copy simultaneous search method

21 January 2018

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Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs.

21 January 2018

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Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations

21 January 2018

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21 January 2018

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Computational fragment-based binding site identification by ligand competitive saturation

21 January 2018

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Protein flexibility in docking and surface mapping

21 January 2018

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Molecular recognition and ligand association

21 January 2018

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Solvent fluctuations in hydrophobic cavity-ligand binding kinetics

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

Improving protocols for protein mapping through proper comparison to crystallography data

21 January 2018

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Full protein flexibility is essential for proper hot-spot mapping.

21 January 2018

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Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics

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21 January 2018

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21 January 2018

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21 January 2018

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De novo ligand design with explicit water molecules: an application to bacterial neuraminidase.

21 January 2018

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Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

21 January 2018

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Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

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Classification of water molecules in protein binding sites.

21 January 2018

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Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

Targeting conserved water molecules: design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

Free enthalpies of replacing water molecules in protein binding pockets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4).

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

Discovery of a Novel Chemotype of Tyrosine Kinase Inhibitors by Fragment-Based Docking and Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

Optimization of inhibitors of the tyrosine kinase EphB4. 2. Cellular potency improvement and binding mode validation by X-ray crystallography

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

The use of AlphaScreen technology in HTS: current status

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

The protein data bank: A computer-based archival file for macromolecular structures

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

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

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

GROMACS: fast, flexible, and free

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

Comparison of simple potential functions for simulating liquid water

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

Canonical sampling through velocity rescaling

21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

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21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

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21 January 2018

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https://api.crossref.org/works/10.1002%2FCMDC.201300156

Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

7 January 2021

Hydrophobicity at the surface of proteins

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

7 January 2021

Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

7 January 2021

The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

7 January 2021

Understanding kinase selectivity through energetic analysis of binding site waters

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201300156

7 January 2021

Identifiers

DOI

10.1002/CMDC.201300156

1 reference

4 December 2017

1 reference