Related references
Note: Only part of the references are listed.Catalytic Mechanism of Aromatic Prenylation by NphB
Yue Yang et al.
BIOCHEMISTRY (2012)
Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure-Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis
Falgun Shah et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations
Riccardo Baron et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
Thijs Beuming et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)
Application of MM-GB/SA and WaterMap to SRC Kinase Inhibitor Potency Prediction
Anna Kohlmann et al.
ACS MEDICINAL CHEMISTRY LETTERS (2012)
Structure-activity relationship study of 2,4-diaminothiazoles as Cdk5/p25 kinase inhibitors
Joydev K. Laha et al.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2011)
Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases
Robert Abel et al.
CHEMMEDCHEM (2011)
Finding a better path to drug selectivity
Yuko Kawasaki et al.
DRUG DISCOVERY TODAY (2011)
Discovery and Structure-Activity Relationship of 3-Aminopyrid-2-ones as Potent and Selective Interleukin-2 Inducible T-Cell Kinase (Itk) Inhibitors
Jean-Damien Charrier et al.
JOURNAL OF MEDICINAL CHEMISTRY (2011)
A Role for Hydration in Interleukin-2 Inducible T Cell Kinase (Itk) Selectivity
Ronald M. A. Knegtel et al.
MOLECULAR INFORMATICS (2011)
Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase
Phillip W. Snyder et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Ligand binding to protein-binding pockets with wet and dry regions
Lingle Wang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Understanding Kinase Selectivity Through Energetic Analysis of Binding Site Waters
Daniel D. Robinson et al.
CHEMMEDCHEM (2010)
Addressing Limitations with the MM-GB/SA Scoring Procedure using the Water Map Method and Free Energy Perturbation Calculations
Cristiano R. W. Guimaraes et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)
How Can Hydrophobic Association Be Enthalpy Driven?
Piotr Setny et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors
James Luccarelli et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Julien Michel et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2010)
Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6
Jill E. Chrencik et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
Free Energy, Entropy, and Enthalpy of a Water Molecule in Various Protein Environments
Hongtao Yu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Water in Cavity-Ligand Recognition
Riccardo Baron et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
DRUG DISCOVERY Priming the antimalarial pipeline
David A. Fidock
NATURE (2010)
MOLECULAR BINDING Under water's influence
Gerhard Hummer
NATURE CHEMISTRY (2010)
No difference in kinetics of tau or histone phosphorylation by CDK5/p25 versus CDK5/p35 in vitro
Dylan W. Peterson et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor
Christopher Higgs et al.
ACS MEDICINAL CHEMISTRY LETTERS (2010)
Dewetting and Hydrophobic Interaction in Physical and Biological Systems
Bruce J. Berne et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2009)
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface
Sergio Wong et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Prediction of the Water Content in Protein Binding Sites
Julien Michel et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
The Properties of Water: Insights from Quantum Simulations
Francesco Paesani et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Free Energies and Entropies of Water Molecules at the Inhibitor-Protein Interface of DNA Gyrase
Hongtao Yu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization
Julien Michel et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
High-energy water sites determine peptide binding affinity and specificity of PDZ domains
Thijs Beuming et al.
PROTEIN SCIENCE (2009)
MM-GB/SA rescoring of docking poses in structure-based lead optimization
Cristiano R. W. Guimaraes et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)
Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
Robert Abel et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Solvent molecules bridge the mechanical unfolding transition state of a protein
Lorna Dougan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor
Chongfeng Pan et al.
JOURNAL OF MEDICINAL CHEMISTRY (2007)
Classification of water molecules in protein binding sites
Caterina Barillari et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes
Yipin Lu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)
Molecular biology of PCSK9: its role in LDL metabolism
Jay D. Horton et al.
TRENDS IN BIOCHEMICAL SCIENCES (2007)
Strengths of hydrogen bonds involving phosphorylated amino acid side chains
Daniel J. Mandell et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
Tom Young et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Chemogenomics: structuring the drug discovery process to gene families
C. John Harris et al.
DRUG DISCOVERY TODAY (2006)
Hydration thermodynamic properties of amino acid analogues: A systematic comparison of biomolecular force fields and water models
Berk Hess et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Opinion - Drug-target residence time and its implications for lead optimization
Robert A. Copeland et al.
NATURE REVIEWS DRUG DISCOVERY (2006)
Adenosine receptors as therapeutic targets
KA Jacobson et al.
NATURE REVIEWS DRUG DISCOVERY (2006)
Structural basis of Src tyrosine kinase inhibition with a new class of potent and selective trisubstituted purine-based compounds
D Dalgarno et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2006)
A general purpose model for the condensed phases of water: TIP4P/2005
JLF Abascal et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Electrostatic influence of active-site waters on the nucleophilic aromatic substitution catalyzed by 4-chlorobenzoyl-CoA dehalogenase
DG Xu et al.
FEBS LETTERS (2005)
Derivation and evaluation of a flexible SPC model for liquid water
S Amira et al.
CHEMICAL PHYSICS (2004)
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
HW Horn et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Flexible TIP4P model for molecular dynamics simulation of liquid water
CP Lawrence et al.
CHEMICAL PHYSICS LETTERS (2003)
Origins of PDZ domain ligand specificity - Structure determination and mutagenesis of the erbin PDZ domain
NJ Skelton et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
Thermodynamics of protein folding: a microscopic view
T Lazaridis et al.
BIOPHYSICAL CHEMISTRY (2003)
The protein kinase complement of the human genome
G Manning et al.
SCIENCE (2002)
Serine protease mechanism and specificity
L Hedstrom
CHEMICAL REVIEWS (2002)
An examination of the five-site potential (TIP5P) for water
M Lísal et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
A reappraisal of what we have learnt during three decades of computer simulations on water
B Guillot
JOURNAL OF MOLECULAR LIQUIDS (2002)
Protein-water interactions in a dynamic world
C Mattos
TRENDS IN BIOCHEMICAL SCIENCES (2002)
Protein folding mediated by solvation:: Water expulsion and formation of the hydrophobic core occur after the structural collapse
MS Cheung et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
P Mark et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2001)
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
GA Kaminski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2001)
Residence times of water molecules in the hydration sites of myoglobin
VA Makarov et al.
BIOPHYSICAL JOURNAL (2000)
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
PA Kollman et al.
ACCOUNTS OF CHEMICAL RESEARCH (2000)
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
MW Mahoney et al.
JOURNAL OF CHEMICAL PHYSICS (2000)
A ligand that is predicted to bind better to avidin than biotin: Insights from computational fluorine scanning
B Kuhn et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)
Molecular dynamics simulations of nucleic acids with a generalized born solvation model
V Tsui et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)