J. Nielsen

发表

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.

L. Serrano, R. Guérois, J. Nielsen, 2002, Journal of molecular biology.

Fast empirical pKa prediction by Ewald summation.

G. Vriend, E. Krieger, J. Nielsen, 2006, Journal of molecular graphics & modelling.

J. Nielsen, 2003 .

The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins

J. Nielsen, M. Gunner, B. García-Moreno E., 2011, Proteins.

Analyzing enzymatic pH activity profiles and protein titration curves using structure-based pKa calculations and titration curve fitting.

J. Nielsen, 2009, Methods in enzymology.

Analyzing Protein NMR pH-Titration Curves

J. Nielsen, 2008 .

Calculating pKa values in enzyme active sites

J. Mccammon, J. Nielsen, J. McCammon, 2003, Protein science : a publication of the Protein Society.

Optimizing the hydrogen‐bond network in Poisson–Boltzmann equation‐based pKa calculations

G. Vriend, J. Nielsen, 2001, Proteins.

Electrostatics in the active site of an alpha-amylase.

T. Borchert, J. Nielsen, D. Otzen, 1999, European journal of biochemistry.

Titration_DB: Storage and analysis of NMR‐monitored protein pH titration curves

J. Nielsen, L. McIntosh, P. B. Crowley, 2010, Proteins.

Determination of electrostatic interaction energies and protonation state populations in enzyme active sites.

Chresten R. Søndergaard, G. Pollastri, J. Nielsen, 2008, Journal of molecular biology.

The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase.

J. Nielsen, R. Wierenga, V. Filimonov, 2000, European journal of biochemistry.

The active site cysteine of ubiquitin-conjugating enzymes has a significantly elevated pKa: functional implications.

J. Nielsen, B. Miller, Helen Webb, 2005, Biochemistry.

Rewarding Cancer Research

Nathan A. Baker, Todd J. Dolinsky, G. Klebe, 1996, Environmental Health Perspectives.

Highly perturbed pKa values in the unfolded state of hen egg white lysozyme.

J. Nielsen, D. Farrell, F. O'Meara, 2012, Biophysical journal.

Calculating pKa values in the cAMP‐dependent protein kinase: The effect of conformational change and ligand binding

J. Nielsen, Una Bjarnadottir, 2010, Protein science : a publication of the Protein Society.

Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies

Barbara M. Tynan-Connolly, Michael A. Johnston, Chresten R. Søndergaard, 2010, Nucleic acids research.

Running title : Protein electrostatics

J. Nielsen, Predrag Kuki, 2017 .

Probing electrostatic interactions along the reaction pathway of a glycoside hydrolase: histidine characterization by NMR spectroscopy.

S. Withers, J. Nielsen, M. Schubert, 2007, Biochemistry.

Analysis of an industrial production suspension of Bacillus lentus subtilisin crystals by powder diffraction: a powerful quality-control tool.

J. Nielsen, K. Wilson, J. Turkenburg, 2014, Acta crystallographica. Section D, Biological crystallography.

Structure of a GH51 α-l-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi

M. Artola, J. Nielsen, J. Turkenburg, 2020, Acta crystallographica. Section D, Structural biology.

Coupled effect of salt and pH on proteins probed with NMR spectroscopy

J. Nielsen, Predrag Kukic, C. Hewage, 2013 .

Heparin Enhances Serpin Inhibition of the Cysteine Protease Cathepsin L*

J. Nielsen, Piotr S. Kowalski, D. Worrall, 2009, The Journal of Biological Chemistry.

Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.

S. Gåseidnes, B. Synstad, G. Vriend, 2004, European journal of biochemistry.

Prolyl hydroxylase-1 negatively regulates IkappaB kinase-beta, giving insight into hypoxia-induced NFkappaB activity.

J. Nielsen, J. Pouysségur, E. Cummins, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Structural Dynamics and Catalytic Properties of a Multi-Modular Xanthanase

Svendsen, Kasper, B. Henrissat, 2020 .

A study of Glacial Isostatic Adjustment in Greenland

J. Nielsen, G. Spada, G. Aðalgeirsdóttir, 2010 .

Protein engineering of bacterial α-amylases

T. Borchert, J. Nielsen, 2000 .

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

Gerhard Klebe, Nathan A. Baker, Jan H. Jensen, 2007, Nucleic Acids Res..

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

Nathan A. Baker, James Andrew McCammon, Todd J. Dolinsky, 2004, Nucleic Acids Res..

Chronic Occupational Ray Poisoning; a Discussion Based on a Case of Leucemia in a Radium Worker

J. Nielsen, 1932 .

Improvements to the APBS biomolecular solvation software suite

Jiahui Chen, Guo-Wei Wei, Nathan A. Baker, 2017, Protein science : a publication of the Protein Society.

Web servers and services for electrostatics calculations with APBS and PDB2PQR

Robert M. Hanson, Yong Huang, Nathan A. Baker, 2011, J. Comput. Chem..

Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution

J. Nielsen, D. Shields, Nora Khaldi, 2011, Proteins.

Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase.

M. D. Joshi, S. Withers, J. Nielsen, 2001, Biochemistry.

The determinants of α-amylase pH–activity profiles

G. Vriend, T. Borchert, J. Nielsen, 2001 .

Prolyl hydroxylase-1 negatively regulates IκB kinase-β, giving insight into hypoxia-induced NFκB activity

J. Nielsen, J. Pouysségur, E. Cummins, 2006, Proceedings of the National Academy of Sciences.

Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase.

S. Withers, J. Nielsen, L. McIntosh, 2013, Biochemistry.

Rational engineering of the stability and the catalytic performance of enzymes

S. Gåseidnes, B. Synstad, J. Nielsen, 2003 .

Protein engineering of bacterial alpha-amylases.

T. Borchert, J. Nielsen, 2000, Biochimica et biophysica acta.

Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity.

J. Nielsen, L. Lo Leggio, A. Svendsen, 2019, Cell chemical biology.

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity

Xiaoyu Zhang, Chandrajit L. Bajaj, Nathan A. Baker, 2006, Multiscale Model. Simul..

Integrated prediction of the effect of mutations on multiple protein characteristics

Michael A. Johnston, Chresten R. Søndergaard, J. Nielsen, 2011, Proteins.

Constructing and Evaluating Predictive Models for Protein Biophysical Characteristics

Jens Erik Nielsen, Michael A. Johnston, Michael Johnston, 2011 .

Improving the analysis of NMR spectra tracking pH‐induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift

Chresten R. Søndergaard, G. Pollastri, J. Nielsen, 2010, Proteins.

Redesigning protein pKa values

Barbara M. Tynan-Connolly, J. Nielsen, 2006, Protein science : a publication of the Protein Society.

Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis

Shanshan Wu, Keith S. Wilson, Kaare Teilum, 2020, PeerJ.

Protein dielectric constants determined from NMR chemical shift perturbations.

Damien Farrell, Jens Erik Nielsen, Kaare Teilum, 2013, Journal of the American Chemical Society.

Toward fast determination of protein stability maps: experimental and theoretical analysis of mutants of a Nocardiopsis prasina serine protease.

Thomas A. Poulsen, Michael A. Johnston, T. Borchert, 2012, Biochemistry.

Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations

M. D. Joshi, J. Nielsen, L. McIntosh, 2011, Journal of biomolecular NMR.

Details in the Reaction Mechanism of Chitinases

B. Synstad, J. Nielsen, D. Komander, 2003 .

Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations

Predrag Kukic, Jens Erik Nielsen, Piyanat Meekrathok, 2017, J. Chem. Inf. Model..

Predicting the open conformations of protein kinases using molecular dynamics simulations.

J. Nielsen, Una Bjarnadottir, 2012, Biopolymers.

On the evaluation and optimization of protein X‐ray structures for pKa calculations

J. Mccammon, J. Nielsen, J. Andrew McCammon, 2003, Protein science : a publication of the Protein Society.

Electrostatics in proteins and protein-ligand complexes.

Jens Erik Nielsen, J. Nielsen, Predrag Kukić, 2010, Future medicinal chemistry.

On the development of protein pKa calculation algorithms

Nathan A. Baker, Damien Farrell, Jens Erik Nielsen, 2011, Proteins.

Remeasuring HEWL pKa values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pKa calculations

Damien Farrell, Helen Webb, Kaare Teilum, 2011, Proteins.

The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide.

E. Krieger, J. Nielsen, J. E. V. van Leeuwen, 2006, The Biochemical journal.

The Effects of Modifying the Surface Charge on the Catalytic Activity of a Thermolysin-like Protease*

V. Eijsink, B. van den Burg, G. Vriend, 2002, The Journal of Biological Chemistry.

PROGRESS IN THE PREDICTION OF pK a VALUES IN PROTEINS

Nathan A. Baker, Emil Alexov, Damien Farrell, 2011 .

Improving macromolecular electrostatics calculations.

G Klebe, B Honig, G Vriend, 1999, Protein engineering.

Transport tax reforms, two-part tariffs, and revenue recycling - A theoretical result

J. Nielsen, 2006 .

Optimal taxation and congestion externalities in a model of household time allocation

J. Nielsen, Ninette Pilegaard, 2005 .

pKD: re-designing protein pKa values

Jens Erik Nielsen, Barbara M. Tynan-Connolly, J. Nielsen, 2006, Nucleic Acids Res..

A collaborative environment for developing and validating predictive tools for protein biophysical characteristics

Damien Farrell, Jens Erik Nielsen, Michael A. Johnston, 2012, Journal of Computer-Aided Molecular Design.

Analysing the pH-dependent properties of proteins using pKa calculations.

J. Nielsen, 2007, Journal of molecular graphics & modelling.

Electrostatics in proteins and protein-ligand complexes.

J. Nielsen, P. Kukic, 2010, Future medicinal chemistry.

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

Nathan A. Baker, Jan H. Jensen, Todd J. Dolinsky, 2007, Nucleic Acids Res..

Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase.

S. Withers, J. Nielsen, L. McIntosh, 2013, Biochemistry.

Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions.

Gianluca Pollastri, Jens Erik Nielsen, Chresten R. Søndergaard, 2009, Journal of medicinal chemistry.

Probing electrostatic interactions along the reaction pathway of a glycoside hydrolase: histidine characterization by NMR spectroscopy.

S. Withers, J. Nielsen, M. Schubert, 2007, Biochemistry.

The determinants of alpha-amylase pH-activity profiles.

G. Vriend, T. Borchert, J. Nielsen, 2001, Protein engineering.