PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. - Todd J. Dolinsky; Jens Erik Nielsen; James Andrew McCammon; Nathan A. Baker (Nucleic Acids Res., 2004)

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity. - Xiaoyu Zhang 011; Chandrajit L. Bajaj; Bong June Kwon; Todd J. Dolinsky; Jens Erik Nielsen; Nathan A. Baker (Multiscale Model. Simul., 2006)

pKD: re-designing protein pKa values. - Barbara M. Tynan-Connolly; Jens Erik Nielsen (Nucleic Acids Res., 2006)

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. - Todd J. Dolinsky; Paul Czodrowski; Hui Li; Jens Erik Nielsen; Jan H. Jensen; Gerhard Klebe; Nathan A. Baker (Nucleic Acids Res., 2007)

Web servers and services for electrostatics calculations with APBS and PDB2PQR. - Samir Unni; Yong Huang; Robert M. Hanson; Malcolm Tobias; Sriram Krishnan; Wilfred W. Li; Jens Erik Nielsen; Nathan A. Baker (J. Comput. Chem., 2011)

LigpKa - a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations. - Paul Czodrowski; Chresten R. Søndergaard; Sebastian Dohm; Gerhard Klebe; Jens Erik Nielsen (J. Cheminformatics, 2011)

A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. - Michael A. Johnston; Damien Farrell; Jens Erik Nielsen (J. Comput. Aided Mol. Des., 2012)

DataPipeline: Automated importing and fitting of large amounts of biophysical data. - Damien Farrell; Jens Erik Nielsen (J. Comput. Chem., 2012)

Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations. - Piyanat Meekrathok; Predrag Kukic; Jens Erik Nielsen; Wipa Suginta (J. Chem. Inf. Model., 2017)