| PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations TJ Dolinsky, JE Nielsen, JA McCammon, NA Baker Nucleic acids research 32 (suppl_2), W665-W667, 2004 | 3818 | 2004 |
| PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations TJ Dolinsky, P Czodrowski, H Li, JE Nielsen, JH Jensen, G Klebe, ... Nucleic acids research 35 (suppl_2), W522-W525, 2007 | 2110 | 2007 |
| Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations R Guerois, JE Nielsen, L Serrano Journal of molecular biology 320 (2), 369-387, 2002 | 1983 | 2002 |
| Improvements to the APBS biomolecular solvation software suite E Jurrus, D Engel, K Star, K Monson, J Brandi, LE Felberg, DH Brookes, ... Protein Science 27 (1), 112-128, 2018 | 1939 | 2018 |
| Prolyl hydroxylase-1 negatively regulates IκB kinase-β, giving insight into hypoxia-induced NFκB activity EP Cummins, E Berra, KM Comerford, A Ginouves, KT Fitzgerald, ... Proceedings of the National Academy of Sciences 103 (48), 18154-18159, 2006 | 947 | 2006 |
| Fast empirical pKa prediction by Ewald summation E Krieger, JE Nielsen, CAEM Spronk, G Vriend Journal of Molecular Graphics and Modelling 25 (4), 481-486, 2006 | 469 | 2006 |
| Protein engineering of bacterial α-amylases JE Nielsen, TV Borchert Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular …, 2000 | 458 | 2000 |
| Web servers and services for electrostatics calculations with APBS and PDB2PQR S Unni, Y Huang, RM Hanson, M Tobias, S Krishnan, WW Li, JE Nielsen, ... Journal of computational chemistry 32 (7), 1488-1491, 2011 | 299 | 2011 |
| Progress in the prediction of pKa values in proteins E Alexov, EL Mehler, N Baker, A M. Baptista, Y Huang, F Milletti, ... Proteins: structure, function, and bioinformatics 79 (12), 3260-3275, 2011 | 289 | 2011 |
| Optimizing the hydrogen‐bond network in Poisson–Boltzmann equation‐based pKa calculations JE Nielsen, G Vriend Proteins: Structure, Function, and Bioinformatics 43 (4), 403-412, 2001 | 256 | 2001 |
| Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase B Synstad, S Gåseidnes, DMF Van Aalten, G Vriend, JE Nielsen, ... European journal of biochemistry 271 (2), 253-262, 2004 | 228 | 2004 |
| Calculating pKa values in enzyme active sites JE Nielsen, JA McCammon Protein science 12 (9), 1894-1901, 2003 | 200 | 2003 |
| Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase MD Joshi, G Sidhu, JE Nielsen, GD Brayer, SG Withers, LP McIntosh Biochemistry 40 (34), 10115-10139, 2001 | 171 | 2001 |
| On the evaluation and optimization of protein X‐ray structures for pKa calculations JE Nielsen, JA McCammon Protein science 12 (2), 313-326, 2003 | 148 | 2003 |
| Improving macromolecular electrostatics calculations JE Nielsen, KV Andersen, B Honig, RWW Hooft, G Klebe, G Vriend, ... Protein engineering 12 (8), 657-662, 1999 | 144 | 1999 |
| The determinants of α-amylase pH–activity profiles JE Nielsen, TV Borchert, G Vriend Protein engineering 14 (7), 505-512, 2001 | 139 | 2001 |
| The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins JE Nielsen, MR Gunner, B García‐Moreno E Proteins: Structure, Function, and Bioinformatics 79 (12), 3249-3259, 2011 | 122 | 2011 |
| Remeasuring HEWL pKa values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pKa calculations H Webb, BM Tynan‐Connolly, GM Lee, D Farrell, F O'Meara, ... Proteins: Structure, Function, and Bioinformatics 79 (3), 685-702, 2011 | 122 | 2011 |
| Electrostatics in proteins and protein-ligand complexes P Kukic, JE Nielsen Future Medicinal Chemistry 2 (4), 647-666, 2010 | 116 | 2010 |
| Protein dielectric constants determined from NMR chemical shift perturbations P Kukic, D Farrell, LP McIntosh, B García-Moreno E, KS Jensen, Z Toleikis, ... Journal of the American Chemical Society 135 (45), 16968-16976, 2013 | 97 | 2013 |
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