Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria

In Silico Investigation of pH-Dependence of Prolactin and Human Growth Hormone Binding to Human Prolactin Receptor

(2016) Lin Wang et al.   Communications in Computational Physics

BACE1 (β-secretase) inhibitors for the treatment of Alzheimer's disease

(2014) Arun K. Ghosh et al.   CHEMICAL SOCIETY REVIEWS

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) Jason M. Swails et al.   Journal of Chemical Theory and Computation

Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

(2014) M. Olivia Kim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

The Role of Protonation States in Ligand-Receptor Recognition and Binding

(2013) Marharyta Petukh et al.   CURRENT PHARMACEUTICAL DESIGN

On the Active Site Protonation State in Aspartic Proteases: Implications for Drug Design

(2013) Fredy Sussman et al.   CURRENT PHARMACEUTICAL DESIGN

pH-Dependent Dynamics of Complex RNA Macromolecules

(2013) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Improved Generalized Born Solvent Model Parameters for Protein Simulations

(2013) Hai Nguyen et al.   Journal of Chemical Theory and Computation

Toward Accurate Prediction of the Protonation Equilibrium of Nucleic Acids

(2013) Garrett B. Goh et al.   Journal of Physical Chemistry Letters

Deconstructing Activation Events in Rhodopsin

(2013) Elena N. Laricheva et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations

(2013) Predrag Kukic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protonation and pK changes in protein–ligand binding

(2013) Alexey V. Onufriev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study

(2012) Arghya Barman et al.   Journal of Chemical Information and Modeling

Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics

(2012) Jason M. Swails et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

(2012) Natali V. Di Russo et al.   PLoS Computational Biology

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

(2011) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Large shifts in pKa values of lysine residues buried inside a protein

(2011) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of tyrosine 71 in modulating the flap conformations of BACE1

(2011) Steven A. Spronk et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress in the prediction of pKa values in proteins

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

pH replica-exchange method based on discrete protonation states

(2011) Satoru G. Itoh 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

Conformational Consequences of Ionization of Lys, Asp, and Glu Buried at Position 66 in Staphylococcal Nuclease

(2010) Daniel A. Karp et al.   BIOCHEMISTRY

Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1

(2010) José L. Domínguez et al.   BIOCHEMISTRY

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

(2010) Boris Aguilar et al.   BIOPHYSICAL JOURNAL

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

(2010) Sarah L. Williams et al.   Journal of Chemical Theory and Computation

The SAMPL2 blind prediction challenge: introduction and overview

(2010) Matthew T. Geballe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Charges in the hydrophobic interior of proteins

(2010) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease

(2010) Joanna Trylska 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

Discovery of aminoheterocycles as a novel β-secretase inhibitor class: pH dependence on binding activity part 1

(2009) Shawn J. Stachel et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Cell biology, regulation and inhibition of β-secretase (BACE-1)

(2009) Clare E. Hunt et al.   FEBS Journal

The  -Secretase Enzyme BACE in Health and Alzheimer's Disease: Regulation, Cell Biology, Function, and Therapeutic Potential

(2009) R. Vassar et al.   JOURNAL OF NEUROSCIENCE

A fast and accurate computational approach to protein ionization

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

Probing electric fields in proteins in solution by NMR spectroscopy

(2008) Mathias A. S. Hass et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Determination of Electrostatic Interaction Energies and Protonation State Populations in Enzyme Active Sites

(2007) Chresten R. Søndergaard et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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