Correlating Structure and Energetics in Protein-Ligand Interactions: Paradigms and Paradoxes

Structural and thermodynamic studies of binding saturated fatty acids to bovine β-lactoglobulin

(2012) Joanna I. Loch et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Recognizing Pitfalls in Virtual Screening: A Critical Review

(2012) Thomas Scior et al.   Journal of Chemical Information and Modeling

Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations

(2012) Yue Shi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein activity regulation by conformational entropy

(2012) Shiou-Ru Tzeng et al.   NATURE

PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements

(2011) Yat T. Tang et al.   Journal of Chemical Information and Modeling

Protein–Ligand Interactions: Thermodynamic Effects Associated with Increasing Nonpolar Surface Area

(2011) James M. Myslinski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2011) Jasmin Mecinović et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

(2011) P. W. Snyder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ligand binding to protein-binding pockets with wet and dry regions

(2011) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extent of enthalpy-entropy compensation in protein-ligand interactions

(2011) Tjelvar S. G. Olsson et al.   PROTEIN SCIENCE

Virtual screening using molecular simulations

(2011) Tianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Purposely engineered drug–target mismatches for entropy-based drug optimization

(2011) Ariel Fernández et al.   TRENDS IN BIOTECHNOLOGY

Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: Binding of phosphonamidate to the S1'-pocket of thermolysin

(2010) L. Englert et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Hydrophobic Side Chain Dynamics of a Glutamate Receptor Ligand Binding Domain

(2010) Alexander S. Maltsev et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein−Ligand Binding Affinity

(2010) Seth A. Hayik et al.   Journal of Chemical Theory and Computation

How Can Hydrophobic Association Be Enthalpy Driven?

(2010) Piotr Setny et al.   Journal of Chemical Theory and Computation

Enhancement of Hydrophobic Interactions and Hydrogen Bond Strength by Cooperativity: Synthesis, Modeling, and Molecular Dynamics Simulations of a Congeneric Series of Thrombin Inhibitors

(2010) Laveena Muley et al.   JOURNAL OF MEDICINAL CHEMISTRY

A Medicinal Chemist’s Guide to Molecular Interactions

(2010) Caterina Bissantz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

(2010) Bernhard Baum et al.   JOURNAL OF MOLECULAR BIOLOGY

Lactose Binding to Galectin-1 Modulates Structural Dynamics, Increases Conformational Entropy, and Occurs with Apparent Negative Cooperativity

(2010) Irina V. Nesmelova et al.   JOURNAL OF MOLECULAR BIOLOGY

Congeneric but Still Distinct: How Closely Related Trypsin Ligands Exhibit Different Thermodynamic and Structural Properties

(2010) Tobias Brandt et al.   JOURNAL OF MOLECULAR BIOLOGY

Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy−Entropy Compensation in SH2−Ligand Binding

(2010) Joshua M. Ward et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

(2010) Carl Diehl et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of conformational entropy in molecular recognition by calmodulin

(2010) Michael S Marlow et al.   Nature Chemical Biology

Thermodynamic and Structural Effects of Macrocyclic Constraints in Protein−Ligand Interactions

(2010) John E. DeLorbe et al.   ACS Medicinal Chemistry Letters

The binding cavity of mouse major urinary protein is optimised for a variety of ligand binding modes

(2009) Thelma A. Pertinhez et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

How Much Binding Affinity Can be Gained by Filling a Cavity?

(2009) Yuko Kawasaki et al.   Chemical Biology & Drug Design

Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3

(2009) Carl Diehl et al.   JOURNAL OF BIOMOLECULAR NMR

More than a Simple Lipophilic Contact: A Detailed Thermodynamic Analysis of Nonbasic Residues in the S1 Pocket of Thrombin

(2009) Bernhard Baum et al.   JOURNAL OF MOLECULAR BIOLOGY

Thermodynamic and Structural Effects of Conformational Constraints in Protein−Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization

(2009) John E. DeLorbe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Adding calorimetric data to decision making in lead discovery: a hot tip

(2009) John E. Ladbury et al.   NATURE REVIEWS DRUG DISCOVERY

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Conformational constraint in protein ligand design and the inconsistency of binding entropy

(2008) D. Gomika Udugamasooriya et al.   BIOPOLYMERS

How Do Halogen Substituents Contribute to Protein-Binding Interactions? A Thermodynamic Study of Peptide Ligands with Diverse Aryl Halides

(2008) Adnan Memic et al.   CHEMBIOCHEM

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

(2008) Tjelvar S.G. Olsson et al.   JOURNAL OF MOLECULAR BIOLOGY

Residual Ligand Entropy in the Binding ofp-Substituted Benzenesulfonamide Ligands to Bovine Carbonic Anhydrase II

(2008) Henning Stöckmann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Heat capacity changes upon burial of polar and nonpolar groups in proteins

(2002) Vakhtang V. Loladze et al.   PROTEIN SCIENCE