Publications

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Contents

Refereed Journal articles and refereed reviews

1999

  1. Improving macromolecular electrostatics calculations
    Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC
    Protein Eng 1999 Aug;12(8):657-62
  2. Electrostatics in the active site of an alpha-amylase.
    Nielsen JE, Beier L, Otzen D, Borchert TV, Frantzen HB, Andersen KV, Svendsen A
    Eur J Biochem 1999 Sep;264(3):816-24

2000

  1. The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase.
    Lambeir AM, Backmann J, Ruiz-Sanz J, Filimonov V, Nielsen JE, Kursula I, Norledge BV, Wierenga RK
    Eur J Biochem 2000 May;267(9):2516-24
  2. Protein engineering of bacterial alpha-amylases.
    Nielsen JE, Borchert TV
    Biochim Biophys Acta 2000 Dec 29;1543(2):253-274

2001

  1. Optimising the hydrogen-bond network in Poisson-Boltzmann equation based pKa calculations.
    Nielsen JE, Vriend G
    Proteins Volume 43, Issue 4, 2001. Pages: 403-412
  2. The determinants of alpha-amylase pH-activity profiles.
    Nielsen JE, Borchert TV, Vriend G
    Protein Engineering (2001) Jul;14(7) 505-512
  3. Dissecting the Electrostatic Interactions and pH-dependent Activity of a Family 11 Glycosidase.
    Joshi MD, Sidhu G, Nielsen JE, Brayer GD, Withers SG, McIntosh LP
    Biochemistry 2001, 40(34), 10115-10139

2002

  1. The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease.
    Kreij Ad, Burg Bvd, Venema G, Vriend G, Eijsink VGH, Nielsen JE
    J Biol Chem 2002 May 3;277(18):15432-8
  2. Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations.
    Guerois R, Nielsen JE, Serrano L
    J. Mol. Biol. 2002 Jul 5;320(2):369-87

2003

  1. Rational Engineering of the Stability and the Catalytic Performace of Enzymes
    Gaseidnes S, Synstad B, Nielsen JE,, Eijsink VGH
    Journal of Molecular Catalysis B: Enzymatic 21 (2003) 3-8
  2. On the evaluation and optimisation of protein X-ray structures for pKa calculations.
    Nielsen JE, McCammon JA
    Protein Sci 2003 Feb;12(2):313-26
  3. Calculating pKa values in enzyme active sites.
    Nielsen JE, McCammon JA
    Protein Sci (2003) 12:1894-1901

2004

  1. Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.
    Synstad B, Gaseines S,Aalten DMF, Vriend G, Nielsen JE, Eijsink VGH
    Eur. J. Biochem 2004 Jan;271(2):253-62
  2. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.
    Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
    Nucleic Acids Research 2004 Jul 1;32(Web Server issue):W665-7.

2005

  1. The active site cysteine of ubiquitin conjugating enzymes has a significantly elevated pKa: functional implications.
    Tolbert B, Tajc S, Webb H, Snyder J, Nielsen JE, Miller B, Basavappa R
    Biochemistry 2005 Dec 20;44(50):16385-16391

2006

  1. Fast Empirical pKa Prediction by Ewald Summation.
    Krieger E, Nielsen JE, Spronk CAEM, Vriend G
    J Mol Graph Model. 2006 Dec;25(4):481-6.
  2. Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity.
    Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA
    Multiscale Modeling and Simulation 2006 Vol. 5, No. 4, pp. 1196–1213
  3. pKD: Re-Designing protein pKa values.
    Tynan-Connolly BM, Nielsen JE
    Nucleic Acids Research 2006 Jul 1;34(Web Server issue):W48-51.
  4. Analysing the pH-dependent properties of proteins using pKa calculations.
    Nielsen JE
    J Mol Graph Model 2007 Jan;25(5):691-9 Epub 2006 May 19
  5. The human Vps29 retromer component is a metallophosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide.
    Damen E, Krieger E, Nielsen JE, Eygensteyn J, van Leeuwen JEM
    Biochem J. 2006 Sep 15;398(3):399-409
  6. Prolyl hydroxylase-1 negatively regulates I{kappa}B kinase-{beta}, giving insight into hypoxia-induced NF{kappa}B activity.
    Cummins EP, Berra E, Comerford KM, Ginouves A, Fitzgerald KT, Seeballuck F, Godson C, Nielsen JE, Moynagh P, Pouyssegur J, Taylor CT
    Proc. Natl. Acad. Sci. USA, 2006 Nov 28;103(48):18154-9

2007

  1. Re-designing protein pKa values.
    Tynan-Connolly BM, Nielsen JE
    Protein science 2007 Feb;16(2):239-49. Epub 2006 Dec 22.
  2. PDB2PQR - Expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
    Dolinsky T, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker N
    Nucleic Acids Research 2007 Jul 1;35(Web Server issue):W522-5. Epub 2007 May 8.
  3. Probing Electrostatic Interactions along the Reaction Pathway of a Glycoside Hydrolase: Histidine Characterization by NMR Spectroscopy.
    Schubert M, Poon D, Wicki J, Tarling C, Kwan E, Nielsen JE, Withers S, McIntosh L
    Biochemistry 2007 Jun 26;46(25):7383-7395. Epub 2007 Jun 5

2008

  1. Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
    Søndergaard CR, McIntosh LP, Pollastri G, Nielsen JE
    J. Mol. Biol. 2008 Feb 8;376(1):269-87. Epub 2007 Sep 29.

2009

  1. Designed human serum hyaluronidase 1 variant, HYAL1{Delta}L exhibits activity up to pH 5.9
    Reitinger S., Müllegger J., Greiderer B., Nielsen J.E., and Lepperdinger G.
    J. Biol. Chem. 2009 Jul 17;284(29):19173-7. Epub 2009 May 28
  2. Structural artefacts in protein-ligand X-ray structures: implications for the development of docking scoring functions
    Søndergaard C.R., Garrett A., Carstensen T., Pollastri G., Nielsen J.E.
    J. Med. Chem. 2009 Sep 24;52(18):5673-84
  3. Titration_DB: Storage and Analysis of NMR-monitored Protein pH Titration Curves
    Farrell D., Sá-Miranda E., Webb H., Georgi N., Crowley P.B., McIntosh L.P., Nielsen J.E.
    Proteins 2010 Mar;78(4):843-57
  4. Improving the analysis of NMR spectra tracking pH-induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift.
    Kukic P.,Farrell D.,Søndergaard C.R., Bjarnadottir U., Bradley J., Pollastri G., Nielsen J.E.
    Proteins 2010 Mar;78(4):971-84.
  5. Heparin enhances serpin inhibition of the cysteine protease, cathepsin L.
    Higgins W.J., Fox D.M., Kowalski P.S., Nielsen J.E., Worrall D.M.
    J Biol Chem. 2010 Feb 5;285(6):3722-9. Epub 2009 Dec 3.

2010

  1. Electrostatics in proteins and protein-ligand complexes
    Kukic P., Nielsen J.E.
    Future Medicinal Chemistry (in press)


Book chapters, reviews, reports, and other non-refereed publications

  1. On the contribution of conserved acidic residues to the catalytic activity of chitinase B from Serratia marcescens
    Synstad B, Gaseidnes S, Vriend G, Nielsen JE, Eijsink VGH
    Advances in Chitin Science (M.G. Peter, R.A.A. Muzzarelli, A. Domard, eds.), Vol. 4., 2000

  2. Rational (re)engineering of enzymes
    Nielsen JE
    Enzyme functionality: design, engineering, and screening. Ed. Allan Svendsen, Marcel Dekker Inc. New York (2004) ISBN: 0-8247-4709-7

  3. Details in the reaction mechanism of chitinases
    Eijsink VGH, Kolstad G, Gaseidnes S, Synstad B, Peter MG, Nielsen JE, Komander D, Houston D, Aalten DMF
    Enzyme functionality: design, engineering, and screening. Ed. Allan Svendsen, Marcel Dekker Inc. New York (2004) ISBN: 0-8247-4709-7

  4. Predicting protein characteristics from X-ray structures
    Soendergaard C, Nielsen JE
    MPT July 2006


  5. Analyzing Protein NMR pH-Titration Curves
    Nielsen JE
    In: Ralph A. Wheeler and David C. Spellmeyer, editors, Annual Reports in Computational Chemistry, Volume 4. Amsterdam: Elsevier, 2008, p. 89


  6. Analyzing enzymatic pH-activity profiles and protein titration curves using structure-based pKa calculations and titration curve fitting
    Nielsen JE
    In Michael L. Johnson and Ludwig Brand editors: Methods in Enzymology Vol. 454, Burlington: Academic Press, 2009, pp.233-258.


Invited Talks

  1. The 7th IUBMB Conference. Receptor-Ligand Interactions. Bergen, Norway, May 2002
    Title: The substrate specificity of protein kinases


  2. Los Alamos National Laboratory, NM, USA. November 2003
    Title:Homology modelling of Protein Kinases


  3. Queens univesity Belfast, Northern Ireland, UK, 2004
    Title: (Re)-Designing protein pKa values


  4. Reaction Mechanisms VII, Dublin, Ireland. July 4-8 2004
    Title: Designing and analysing pKa values in enzyme Active sites


  5. Phillips Universitaet Marburg, GraduiertenKolleg. June 22nd 2005
    Title: Drugs, washing powder and enzymes: Protein electrostatics and pKa values


  6. Novozymes A/S, Denmark. 29th of May 2006
    Title: Re-designing protein pKa values


  7. University of British Columbia, Vancouver, Canada. August 15th 2006
    Title: Re-designing protein pKa values


  8. Biosys/Danisco A/S, Copenhagen, Denmark. November 1st 2006
    Title: Protein stability and electrostatics


  9. University Cambridge, United Kingdom. November 21st 2006
    Title: Re-designing protein pKa values


  10. University of Copenhagen, Denmark. March 12th 2007
    Title: Reverse protonation in enzyme active sites


  11. Novozymes A/S, Copenhagen, Denmark, 26th of November 2007
    Title: Electrostatic interaction energies in proteins


  12. Lund University, Lund, Sweden, 28th of November 2007
    Title: Measuring electrostatic interaction energies in proteins


  13. University College Cork, Cork, Ireland, 22nd of January 2008
    Title: Measuring electrostatic interaction energies in proteins


  14. University of Birmingham, Birminghan, U.K., 4th of June 2008
    Title: Electrostatics in enzyme active sites


  15. Telluride conference on Protein Electrostatics, Telluride, Colorado, USA, 16th of July 2008
    Title: Prediciting and analysing protein titration curves


  16. Practice Meeting on Advances in Drug Discovery and Development, Bryn Mawr, Philadelphia, PA, USA. 14th-17th of Oct. 2008
    Title: Measuring electrostatic interaction energies in proteins


  17. Novozymes, Copenhagen 5th of December 2008
    Title: Searching and indexing enzyme mutant data with PEAT


  18. University of California, Santa Barbara, 6th of January 2009
    Title: NMR titration ghosts and electrostatic interaction energies


  19. OpenEye EuropCUP III, Toledo Spain. 22nd - 24th of April 2009
    Title: Crystal contacts in protein-ligand complexes


  20. Telluride Workshop on Protein Electrostatics. 6th-10th of July 2009
    Title: Blind predictions and "Forward, downward"


  21. GRC conference on Computer Aided Drug Design. 19th-24th of July, Tilton, NH, USA
    Title: pKa values in proteins and protein-ligand complexes


Poster presentations


  1. NATO/EMBO/FEBS summer school, Spetses, Greece, 1997.
    Nielsen JE, Vriend G
    Title: Optimising macromolecular electrostatic calculations

  2. Third European Symposium of the Protein Society, Garmisch-Partenkirchen, Germany
    Nielsen JE, Vriend G
    Title: Optimising protein pKa calculations

  3. The Lorne conference on protein structure and function. Lorne, Australia, February 1998
    Nielsen JE, Borchert TV, Vriend G
    Title: Electrostatics in the active site of an alpha-amylase

  4. Protein folding dynamics, Ventura CA, January 2002
    Guerous R, Nielsen JE, Serrano L
    Title: Studying protein folding with FOLD-X

  5. Frontiers of structural biology. Keystone conference, Breckenridge, CO, Jan. 2002.
    Nielsen JE, McCammon JA
    Title: Predicting the substrate specificity of protein kinases

  6. 16th Symposium of the Protein Society, August 17-21, 2002, San Diego, CA
    Nielsen JE, McCammon JA
    Title: pKa values in Enzyme Active Sites

  7. 17th Symposium of the Protein Society, July 26-30 2003, Boston, MA.
    Nielsen JE, McCammon JA
    Title: Electrostatics in Enzyme Active Sites

  8. 18th Symposium of the Protein Society, August 14-18 2004, San Diego, CA
    Nielsen JE
    Title: Designing protein pKa values

  9. VIth European Symposium of The Protein Society, April 30th - May 4th 2005, Barcelona, Spain.
    Nielsen JE
    Title:Networks of Electrostatic Interactions in Enzyme Active Sites

  10. MGMS meeting: Biomolecular Simulations : from prediction to practice, Trinity College Dublin Sept 11-14th, 2005
    Bjarnadottir U, Nielsen JE
    Title: Analysing the protein kinase activation process using molecular dynamics simulations

  11. MGMS meeting: Biomolecular Simulations : from prediction to practice, Trinity College Dublin Sept 11-14th, 2005
    Webb H, Nielsen JE
    Title: Proton donor identification using protein pKa calculations

  12. MGMS meeting: Biomolecular Simulations : from prediction to practice, Trinity College Dublin Sept 11-14th, 2005
    Tynan-Connolly B, Nielsen JE
    Title: Re-Designing protein pKa values

  13. MGMS meeting: Biomolecular Simulations : from prediction to practice, Trinity College Dublin Sept 11-14th, 2005
    Agostini L, Nielsen JE
    Title: EATDB: Enzyme Analysis Tool and DataBase

  14. Structure based drug discovery, Whistler, British Columbia, Canada, April 4-9th 2006
    Nielsen JE
    Title: Analysing protein pKa calculations

  15. Indo-French meeting
    Kumar G, Georgi N, Nielsen JE
    Title: Enzyme Analysis Tool and Database (EATDB)

  16. The 20th Symposium of The Protein Society and 20th Anniversity Celebration, San Diego, California, August 5-9, 2006
    Bjarnadottir U, Nielsen JE
    Title: The Protein Kinase Activation Process: A Molecular Dynamics Study

  17. The 16th European Symposium on Quantitative Structure-Activity Relationships & Molecular Modelling The Mediterranean Sea, 10th-17th September 2006
    Sondergaard CR, Pollastri G, Nielsen JE
    Title:Comparing machine learning and empirical methods for scoring of protein-ligand binding energies

  18. Frontiers of NMR in Molecular Biology, Snowbird, Utha, Jan 6-10, 2007
    Carstensen T, Nielsen JE
    Title: Prediction of residues important for protein dynamics. A normal mode analysis approach.

  19. Keystones Conference: Frontiers of NMR in Molecular Biology. Keystones Conference, Snowbird Resort, Snowbird, Utah. Jan 6-10, 2007
    Altering The pKa Values Of HEWL using pKD and 1H-15N HSQC Spectroscopy
    Tynan-Connolly B, Webb H, O'Meara F, McIntosh LP, Nielsen JE

  20. Proteins: From Birth to Death 21st Annual Symposium of The Protein Society, July 21-25, 2007, Boston, MA, USA
    Chresten Soendergaard, Lawrence P. McIntosh, Gianluca Pollastri, Jens Nielsen
    Title: Determination of electrostatic interaction energies and protonation state populations in enzyme active sites by global fits of NMR- titration data and pH-activity profiles.

  21. Proteins: From Birth to Death. 21st Annual Symposium of The Protein Society, July 21-25, 2007, Boston, MA, USA
    Una Bjarnadottir, Tommy Carstensen, Jens Erik Nielsen
    Title: Detailed Analysis of the Dynamics of cAMP Dependent Protein Kinase using Molecular Dynamics Simulations and Normal Mode Analysis.

  22. Proteins: From Birth to Death 21st Annual Symposium of The Protein Society, July 21-25, 2007, Boston, MA, USA
    Georgi N, Farrell D, O’Meara F, Webb H, Tynan-Connolly BM, Bjarnadottir U, Soendergaard C, Nielsen JE
    Title: Structural analysis of datasets from protein engineering studies using PEAT

  23. Proteins: From Birth to Death 21st Annual Symposium of The Protein Society, July 21-25, 2007, Boston, MA, USA
    Bradley J, Salbo R, Nielsen JE
    Title: HEWL Amyloidosis

  24. Proteins: From Birth to Death 21st Annual Symposium of The Protein Society, July 21-25, 2007, Boston, MA, USA
    Tynan-Connolly BM, Nogueira E, O’Meara F, Nielsen JE
    Title: Modifying the pKa values in Hen Egg White Lysozyme using pKD and 1H-15N HSQC Spectroscopy

  25. Protein Kinases & Protein Phosphorylation. July 7-12, 2007 Indian Wells, CA, USA
    Nielsen JE
    Title: Electrostatic decomposition of protein kinase and protein phosphatase structures


  26. UCD Conway Festival, September 20, 2009, Dublin, Ireland
    Carstensen T, Bjarnadottir U, Nielsen JE
    Title: Analysing the determinants of protein dynamics using normal mode analysis


  27. Celebrate the 50th Anniversary of the Determination of the Structure of Myoglobin. VIII European Symposium of The Protein Society Zurich, Switzerland, June 14-18, 2009.
    Predrag Kukić, Damien Farrell, Chresten Søndergaard, Una Bjarnadottir, John Bradley, Gianluca Pollastri , Jens Erik Nielsen
    Title: Improving the analysis of NMR spectra tracking pH-induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift.


  28. Celebrate the 50th Anniversary of the Determination of the Structure of Myoglobin. VIII European Symposium of The Protein Society Zurich, Switzerland, June 14-18, 2009
    Fergal O’Meara, Chresten R. Søndergaard, Michael A. Johnston, Jens Erik Nielsen
    Title: Using an Alanine Scan of Hen Egg White Lysozyme (HEWL) to Validate PEAT-SA.


  29. 21st IUBMB International Congress and 12th FAOBMB Congress of Biochemistry and Molecular Biology, Shanghai, August 2-7, 2009.
    Predrag Kukić, Gianluca Pollastri , Jens Erik Nielsen
    Title: Improving the analysis of NMR spectra by removing artefacts of the electric field.


  30. 21st IUBMB International Congress and 12th FAOBMB Congress of Biochemistry and Molecular Biology, Shanghai, August 2-7, 2009.
    John Bradley, Fergal O'Meara , Jens Erik Nielsen
    Title: Fragmentation Of Hen Lysozyme - Predicted Vs Experimental

  31. Conway Festival Of Science, September 2009.
    M.A. Johnston, F. O'Meara, J.E. Nielsen
    Title: Predicting the effect of point-mutations on the activity of HEWL

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