4.4 Review

Is it the shape of the cavity, or the shape of the water in the cavity?

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Understanding Pre-Structured Motifs (PreSMos) in Intrinsically Unfolded Proteins

Si-Hyung Lee et al.

CURRENT PROTEIN & PEPTIDE SCIENCE (2012)

Editorial Material Physics, Multidisciplinary

Intrinsically disordered proteins

Peter Tompa et al.

PHYSICS TODAY (2012)

Review Chemistry, Multidisciplinary

Aromatic Rings in Chemical and Biological Recognition: Energetics and Structures

Laura M. Salonen et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2011)

Article Chemistry, Medicinal

A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease

Hannes G. Wallnoefer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

AcquaAlta: A Directional Approach to the Solvation of Ligand-Protein Complexes

Gianluca Rossato et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Physical

Dissecting the Energetics of Hydrophobic Hydration of Polypeptides

Silvina Matysiak et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

Article Chemistry, Physical

From Head to Tail: Structure, Solvation, and Hydrogen Bonding of Carboxylate Surfactants at the Organic-Water Interface

Daniel K. Beaman et al.

JOURNAL OF PHYSICAL CHEMISTRY C (2011)

Article Chemistry, Multidisciplinary

Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase

Jasmin Mecinovic et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Biochemistry & Molecular Biology

Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

Moran Grossman et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

Article Multidisciplinary Sciences

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)

Article Multidisciplinary Sciences

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)

Article Biochemistry & Molecular Biology

Extent of enthalpy-entropy compensation in protein-ligand interactions

Tjelvar S. G. Olsson et al.

PROTEIN SCIENCE (2011)

Review Chemistry, Multidisciplinary

Water in the Half Shell: Structure of Water, Focusing on Angular Structure and Solvation

Kim A. Sharp et al.

ACCOUNTS OF CHEMICAL RESEARCH (2010)

Article Biochemistry & Molecular Biology

Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer

S. Zoe Fisher et al.

BIOCHEMISTRY (2010)

Review Chemistry, Multidisciplinary

Vibrational Spectroscopy as a Probe of Structure and Dynamics in Liquid Water

H. J. Bakker et al.

CHEMICAL REVIEWS (2010)

Article Chemistry, Multidisciplinary

Specific Anion Effects on Water Structure Adjacent to Protein Monolayers

Xin Chen et al.

LANGMUIR (2010)

Review Chemistry, Physical

INVITED TOPICAL REVIEW The structure of ambient water

Gary N. I. Clark et al.

MOLECULAR PHYSICS (2010)

Article Biochemistry & Molecular Biology

The role of conformational entropy in molecular recognition by calmodulin

Michael S. Marlow et al.

NATURE CHEMICAL BIOLOGY (2010)

Article Chemistry, Medicinal

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor

Christopher Higgs et al.

ACS MEDICINAL CHEMISTRY LETTERS (2010)

Review Chemistry, Multidisciplinary

Hydrophobic Solvation: A 2D IR Spectroscopic Inquest

Artem A. Bakulin et al.

ACCOUNTS OF CHEMICAL RESEARCH (2009)

Review Chemistry, Physical

Dewetting and Hydrophobic Interaction in Physical and Biological Systems

Bruce J. Berne et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2009)

Review Chemistry, Physical

From Franklin to Today: Toward a Molecular Level Understanding of Bonding and Adsorption at the Oil-Water Interface

Cathryn L. McFearin et al.

JOURNAL OF PHYSICAL CHEMISTRY C (2009)

Article Biochemistry & Molecular Biology

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

Thijs Beuming et al.

PROTEIN SCIENCE (2009)

Review Chemistry, Physical

Water in nonpolar confinement: From nanotubes to proteins and beyond

Jayendran C. Rasaiah et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2008)

Review Chemistry, Multidisciplinary

Water as an active constituent in cell biology

Philip Ball

CHEMICAL REVIEWS (2008)

Review Chemistry, Multidisciplinary

Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding

Vijay M. Krishnamurthy et al.

CHEMICAL REVIEWS (2008)

Article Chemistry, Medicinal

Robust classification of Relevant water molecules in putative protein binding sites

Alessio Amadasi et al.

JOURNAL OF MEDICINAL CHEMISTRY (2008)

Article Biochemistry & Molecular Biology

The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design

Tjelvar S. G. Olsson et al.

JOURNAL OF MOLECULAR BIOLOGY (2008)

Article Chemistry, Multidisciplinary

Negative hyperconjugation of some fluorine containing groups

Otto Exner et al.

NEW JOURNAL OF CHEMISTRY (2008)

Article Multidisciplinary Sciences

Hydrophobicity of protein surfaces: Separating geometry from chemistry

Nicolas Giovambattista et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Chemistry, Physical

Understanding how organic, solvent polarity affects water structure and bonding at halocarbon-water interfaces

Cathryn L. McFearin et al.

JOURNAL OF MOLECULAR LIQUIDS (2007)

Article Chemistry, Multidisciplinary

Specific ion effects on interfacial water structure near macromolecules

Xin Chen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Physics, Multidisciplinary

Observation of immobilized water molecules around hydrophobic groups

Y. L. A. Rezus et al.

PHYSICAL REVIEW LETTERS (2007)

Review Pharmacology & Pharmacy

Water, water everywhere - except where it matters?

Steve W. Homans

DRUG DISCOVERY TODAY (2007)

Review Chemistry, Physical

Hydrogen bonding definitions and dynamics in liquid water

R. Kumar et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Interfacial water structure controls protein conformation

A. Der et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Chemistry, Multidisciplinary

Classification of water molecules in protein binding sites

Caterina Barillari et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Chemistry, Multidisciplinary

Dependence of effective molarity on linker length for an intramolecular protein-ligand system

Vijay M. Krishnamurthy et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Multidisciplinary Sciences

Ligand configurational entropy and protein binding

Chia-en A. Chang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Physics, Multidisciplinary

How water meets a hydrophobic surface

Adele Poynor et al.

PHYSICAL REVIEW LETTERS (2006)

Article Multidisciplinary Sciences

Determination of solvent content in cavities in IL-1β using experimentally phased electron density

Michael L. Quillin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Chemistry, Physical

Confined water: A Mercedes-Benz model study

T Urbic et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Chemistry, Multidisciplinary

Strong solute-solute dispersive interactions in a protein-ligand complex

R Malham et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Multidisciplinary

Enthalpy-entropy compensation is not a general feature of weak association

DM Ford

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Physical

Decreased structure on dissolving methane in water

P Buchanan et al.

CHEMICAL PHYSICS LETTERS (2005)

Review Multidisciplinary Sciences

Interfaces and the driving force of hydrophobic assembly

D Chandler

NATURE (2005)

Article Multidisciplinary Sciences

Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover

S Rajamani et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Chemistry, Physical

Drying and hydrophobic collapse of paraffin plates

XH Huang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Review Biochemistry & Molecular Biology

Modeling water, the hydrophobic effect, and ion solvation

KA Dill et al.

ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE (2005)

Review Materials Science, Multidisciplinary

Investigations of the solid-aqueous interface with vibrational sum-frequency spectroscopy

Adam J. Hopkins et al.

CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE (2005)

Review Chemistry, Multidisciplinary

Molecular recognition in organic crystals: Directed intermolecular bonds or nonlocalized bonding?

JD Dunitz et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2005)

Review Chemistry, Multidisciplinary

Ultrafast guest dynamics in cyclodextrin nanocavities

A Douhal

CHEMICAL REVIEWS (2004)

Article Biochemical Research Methods

Comparative estimation of vibrational entropy changes in proteins through normal modes analysis

BJ Carrington et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2004)

Article Multidisciplinary Sciences

Hydrophobic collapse in multidomain protein folding

RH Zhou et al.

SCIENCE (2004)

Article Chemistry, Organic

The ins and outs of molecular encapsulation

LC Palmer et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2004)

Review Chemistry, Multidisciplinary

Solvation dynamics and proton transfer in supramolecular assemblies

K Bhattacharyya

ACCOUNTS OF CHEMICAL RESEARCH (2003)

Review Chemistry, Multidisciplinary

Interactions with aromatic rings in chemical and biological recognition

EA Meyer et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2003)

Review Chemistry, Multidisciplinary

Binding affinities of host-guest, protein-ligand, and protein-transition-state complexes

KN Houk et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2003)

Article Biochemistry & Molecular Biology

Searching for quantitative entropy-enthalpy compensation among protein variants

JR Beasley et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)

Article Chemistry, Physical

Predicting water's phase diagram and liquid-state anomalies

TM Truskett et al.

JOURNAL OF CHEMICAL PHYSICS (2002)

Article Physics, Multidisciplinary

Hydrogen-bond dynamics near a micellar surface: Origin of the universal slow relaxation at complex aqueous interfaces

S Balasubramanian et al.

PHYSICAL REVIEW LETTERS (2002)

Review Chemistry, Multidisciplinary

Hydrophobic effects and modeling of biophysical aqueous solution interfaces

LR Pratt et al.

CHEMICAL REVIEWS (2002)

Article Multidisciplinary Sciences

Molecular segregation observed in a concentrated alcohol-water solution

S Dixit et al.

NATURE (2002)

Article Multidisciplinary Sciences

Dynamic chemical devices: Modulation of contraction/extension molecular motion by coupled-ion binding/pH change-induced structural switching

M Barboiu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Review Biochemistry & Molecular Biology

Natively unfolded proteins: A point where biology waits for physics

VN Uversky

PROTEIN SCIENCE (2002)

Article Multidisciplinary Sciences

Network of coupled promoting motions in enzyme catalysis

PK Agarwal et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Multidisciplinary Sciences

Enzyme dynamics during catalysis

EZ Eisenmesser et al.

SCIENCE (2002)

Article Multidisciplinary Sciences

Biological water at the protein surface: Dynamical solvation probed directly with femtosecond resolution

SK Pal et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Review Chemistry, Physical

A view of the hydrophobic effect

NT Southall et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2002)

Article Biology

Enthalpy-entropy compensation: a phantom phenomenon

A Cornish-Bowden

JOURNAL OF BIOSCIENCES (2002)

Article Chemistry, Multidisciplinary

Involvement of water in carbohydrate-protein binding

C Clarke et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)

Article Biochemistry & Molecular Biology

Classical molecular interaction potentials:: Improved setup procedure in molecular dynamics simulations of proteins

JL Gelpí et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2001)

Article Physics, Multidisciplinary

Images of nanobubbles on hydrophobic surfaces and their interactions

JWG Tyrrell et al.

PHYSICAL REVIEW LETTERS (2001)

Article Chemistry, Multidisciplinary

Cooperativity in amide hydrogen bonding chains: Implications for protein-folding models

N Kobko et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)

Article Multidisciplinary Sciences

Water at hydrophobic surfaces: Weak hydrogen bonding and strong orientation effects

LF Scatena et al.

SCIENCE (2001)

Article Biochemistry & Molecular Biology

Entropy-enthalpy compensation: Fact or artifact?

K Sharp

PROTEIN SCIENCE (2001)

Review Chemistry, Multidisciplinary

Isokinetic relationship, isoequilibrium relationship, and enthalpy-entropy compensation

L Liu et al.

CHEMICAL REVIEWS (2001)

Article Chemistry, Physical

A high-quality x-ray scattering experiment on liquid water at ambient conditions

G Hura et al.

JOURNAL OF CHEMICAL PHYSICS (2000)

Article Chemistry, Physical

What can x-ray scattering tell us about the radial distribution functions of water?

JM Sorenson et al.

JOURNAL OF CHEMICAL PHYSICS (2000)

Article Biochemistry & Molecular Biology

Structure/thermodynamics relationships of lectin-saccharide complexes -: The Erythrina corallodendron case

GM Bradbrook et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2000)

Review Chemistry, Medicinal

Hydrophobicity:: is LogPo/w more than the sum of its parts?

GE Kellogg et al.

EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2000)

Review Geochemistry & Geophysics

Thermodynamic functions of hydration of hydrocarbons at 298.15 K and 0.1 MPa

AV Plyasunov et al.

GEOCHIMICA ET COSMOCHIMICA ACTA (2000)