Structured Water Molecules in the Binding Site of Bromodomains Can Be Displaced by Cosolvent

Molecular Recognition and Ligand Association

(2013) Riccardo Baron et al.   Annual Review of Physical Chemistry

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

(2013) Katrina W. Lexa et al.   Journal of Chemical Information and Modeling

Solvent fluctuations in hydrophobic cavity–ligand binding kinetics

(2013) Piotr Setny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Nicholas G.M. Davies et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

The bromodomain interaction module

(2012) Panagis Filippakopoulos et al.   FEBS LETTERS

Free enthalpies of replacing water molecules in protein binding pockets

(2012) Sereina Riniker et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Druggability Analysis and Structural Classification of Bromodomain Acetyl-lysine Binding Sites

(2012) Lewis R. Vidler et al.   JOURNAL OF MEDICINAL CHEMISTRY

Optimization of Inhibitors of the Tyrosine Kinase EphB4. 2. Cellular Potency Improvement and Binding Mode Validation by X-ray Crystallography

(2012) Karine Lafleur et al.   JOURNAL OF MEDICINAL CHEMISTRY

Progress in the Development and Application of Small Molecule Inhibitors of Bromodomain–Acetyl-lysine Interactions

(2012) David S. Hewings et al.   JOURNAL OF MEDICINAL CHEMISTRY

Epigenetic protein families: a new frontier for drug discovery

(2012) Cheryl H. Arrowsmith et al.   NATURE REVIEWS DRUG DISCOVERY

Targeting Epigenetic Readers in Cancer

(2012) Mark A. Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Protein flexibility in docking and surface mapping

(2012) Katrina W. Lexa et al.   QUARTERLY REVIEWS OF BIOPHYSICS

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

(2012) Hongtao Zhao et al.   ACS Medicinal Chemistry Letters

Small Molecule Binding to Proteins: Affinity and Binding/Unbinding Dynamics from Atomistic Simulations

(2011) Danzhi Huang et al.   ChemMedChem

RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia

(2011) Johannes Zuber et al.   NATURE

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Thijs Beuming et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Free Energy Landscape of Small Molecule Unbinding

(2011) Danzhi Huang et al.   PLoS Computational Biology

Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant

(2010) Nicolas Basse et al.   CHEMISTRY & BIOLOGY

Understanding Kinase Selectivity Through Energetic Analysis of Binding Site Waters

(2010) Daniel D. Robinson et al.   ChemMedChem

Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping

(2010) Katrina W. Lexa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Binding Site Detection and Druggability Index from First Principles

(2009) Jesus Seco et al.   JOURNAL OF MEDICINAL CHEMISTRY

Flaviviral Protease Inhibitors Identified by Fragment-Based Library Docking into a Structure Generated by Molecular Dynamics

(2009) Dariusz Ekonomiuk et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure-Based Optimization of Potent and Selective Inhibitors of the Tyrosine Kinase Erythropoietin Producing Human Hepatocellular Carcinoma Receptor B4 (EphB4)

(2009) Karine Lafleur et al.   JOURNAL OF MEDICINAL CHEMISTRY

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2009) Kenneth D. Eichenbaum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

(2009) Olgun Guvench et al.   PLoS Computational Biology

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY