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

Biomolecular modeling and simulation: a field coming of age

(2011) Tamar Schlick et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

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

Molecular determinants of the pKavalues of Asp and Glu residues in staphylococcal nuclease

(2009) Carlos A. Castañeda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular simulations of protein dynamics: new windows on mechanisms in biology

(2008) Guy G Dodson et al.   EMBO REPORTS

Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules

(2008) Ramu Anandakrishnan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKavalues

(2008) Michael J. Harms et al.   PROTEIN SCIENCE

A fast and accurate computational approach to protein ionization

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