Protonation and pK changes in protein–ligand binding

pH Optimum of the Photosystem II H2O Oxidation Reaction: Effects of PsbO, the Manganese-Stabilizing Protein, Cl– Retention, and Deprotonation of a Component Required for O2 Evolution Activity

(2012) Alan Commet et al.   BIOCHEMISTRY

Influence of Protonation on Substrate and Inhibitor Interactions at the Active Site of Human Monoamine Oxidase-A

(2012) Gerald Zapata-Torres et al.   Journal of Chemical Information and Modeling

GMCT : A Monte Carlo simulation package for macromolecular receptors

(2012) R. Thomas Ullmann et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Searching of Predictors to Predict pH Optimum of Cellulases

(2011) Shaomin Yan et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs

(2011) Atanu Maiti et al.   DNA REPAIR

HIV gp41 six-helix bundle constructs induce rapid vesicle fusion at pH 3.5 and little fusion at pH 7.0: understanding pH dependence of protein aggregation, membrane binding, and electrostatics, and implications for HIV-host cell fusion

(2011) Kelly Sackett et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Quantum nature of the hydrogen bond

(2011) X.-Z. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Progress in the prediction of pKa values in proteins

(2011) Emil Alexov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins

(2011) Jens E. Nielsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

(2010) Boris Aguilar et al.   BIOPHYSICAL JOURNAL

Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery

(2010) Francesca Milletti et al.   Journal of Chemical Information and Modeling

Development of prolactin receptor antagonists with reduced pH-dependence of receptor binding

(2010) Mathilde J. Kaas Hansen et al.   JOURNAL OF MOLECULAR RECOGNITION

pH-Dependent pKaValues in Proteins—A Theoretical Analysis of Protonation Energies with Practical Consequences for Enzymatic Reactions

(2010) Elisa Bombarda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome

(2010) Xiaoxia Ge et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Alteration of the pH optimum of a family 11 xylanase, XynB6 of Dictyoglomus thermophilum

(2010) M.D. Gibbs et al.   New Biotechnology

Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations

(2010) Nathan J. Palpant et al.   PHYSIOLOGICAL GENOMICS

Calculating pKa values in the cAMP-dependent protein kinase: The effect of conformational change and ligand binding

(2010) Una Bjarnadottir et al.   PROTEIN SCIENCE

In silico modeling of pH-optimum of protein-protein binding

(2010) Rooplekha C. Mitra et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Estimating binding affinities by docking/scoring methods using variable protonation states

(2010) Min-Sun Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein interaction as a predictor of subcellular location

(2009) Chang Jin Shin et al.   BMC Systems Biology

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

(2009) Tim ten Brink et al.   Journal of Chemical Information and Modeling

Regulation of intracellular pH during anoxia in rice coleoptiles in acidic and near neutral conditions

(2009) K. Y. Kulichikhin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Thermodynamic Profiling of HIV RREIIB RNA–Zinc Finger Interactions

(2009) Subrata H. Mishra et al.   JOURNAL OF MOLECULAR BIOLOGY

pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4

(2009) Jason M. Swails et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predicting protein pKaby environment similarity

(2009) Francesca Milletti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Automated site preparation in physics-based rescoring of receptor ligand complexes

(2009) Chaya S. Rapp et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2009) David L. Mobley et al.   STRUCTURE

pH Dependence of Cyanide Binding to the Ferric Heme Domain of the Direct Oxygen Sensor fromEscherichia coliand the Effect of Alkaline Denaturation†

(2008) Anil K. Bidwai et al.   BIOCHEMISTRY

Calculating pH and Salt Dependence of Protein-Protein Binding

(2008) Jan Jensen   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Calculation of absolute protein-ligand binding free energy using distributed replica sampling

(2008) Tomas Rodinger et al.   JOURNAL OF CHEMICAL PHYSICS

Improved pKaprediction: Combining empirical and semimicroscopic methods

(2008) Gernot Kieseritzky et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Calculation of Absolute Ligand Binding Free Energy to a Ribosome-Targeting Protein as a Function of Solvent Model

(2008) Michael S. Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A fast and accurate computational approach to protein ionization

(2008) Velin Z. Spassov et al.   PROTEIN SCIENCE

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Inclusion of ionization states of ligands in affinity calculations

(2008) Serena Donnini et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BIOCHEMISTRY: How Do Proteins Interact?

(2008) D. D. Boehr et al.   SCIENCE

Shifting pH optimum of Bacillus circulans xylanase based on molecular modeling

(2007) Ji Hye Yang et al.   JOURNAL OF BIOTECHNOLOGY

Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors

(2007) Kitiyaporn Wittayanarakul et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein-protein binding is often associated with changes in protonation state

(2007) Aaron C. Mason et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS