Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes

The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States

(2014) Sascha Urbaczek et al.   Journal of Chemical Information and Modeling

Reading PDB: Perception of Molecules from 3D Atomic Coordinates

(2012) Sascha Urbaczek et al.   Journal of Chemical Information and Modeling

NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats

(2011) Sascha Urbaczek et al.   Journal of Chemical Information and Modeling

Web application for studying the free energy of binding and protonation states of protein–ligand complexes based on HINT

(2009) Alexander S. Bayden et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

(2009) Tobias Lippert et al.   Journal of Cheminformatics

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

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS