Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes

Electrostatic and Hydrophobic Interactions Mediate Single-Stranded DNA Recognition and Acta2 Repression by Purine-Rich Element-Binding Protein B

(2016) Amy E. Rumora et al.   BIOCHEMISTRY

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water

(2016) Yandong Huang et al.   Journal of Chemical Theory and Computation

Conformational Activation of a Transmembrane Proton Channel from Constant pH Molecular Dynamics

(2016) Wei Chen et al.   Journal of Physical Chemistry Letters

Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors

(2016) Christopher R. Ellis et al.   Journal of Physical Chemistry Letters

DelPhiPKa web server: predicting pKaof proteins, RNAs and DNAs

(2015) Lin Wang et al.   BIOINFORMATICS

Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence

(2015) Marharyta Petukh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Biophysical and electrochemical studies of protein–nucleic acid interactions

(2015) Richard P. Bowater et al.   MONATSHEFTE FUR CHEMIE

An updated version of NPIDB includes new classifications of DNA–protein complexes and their families

(2015) Olga Zanegina et al.   NUCLEIC ACIDS RESEARCH

pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa

(2015) Lin Wang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BION web server: predicting non-specifically bound surface ions

(2013) Marharyta Petukh et al.   BIOINFORMATICS

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

(2013) Marharyta Petukh et al.   CURRENT PHARMACEUTICAL DESIGN

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Protonation and pK changes in protein–ligand binding

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

Predicting Nonspecific Ion Binding Using DelPhi

(2012) Marharyta Petukh et al.   BIOPHYSICAL JOURNAL

Electrostatic Interactions between Arginines and the Minor Groove in the Nucleosome

(2012) Sean M. West et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Unraveling a Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

(2012) Jason A. Wallace et al.   Journal of Physical Chemistry Letters

NPIDB: nucleic acid—protein interaction database

(2012) Dmitry D. Kirsanov et al.   NUCLEIC ACIDS RESEARCH

Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition

(2011) Junichi Iwakiri et al.   NUCLEIC ACIDS RESEARCH

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

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

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

(2010) Boris Aguilar et al.   BIOPHYSICAL JOURNAL

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

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

How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA

(2010) B. Pan et al.   SCIENCE

Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase

(2009) Kotaro Nakanishi et al.   NATURE

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE