Jens E. Nielsen - Publications

Affiliations: 
Novozymes A/S 
Area:
Protein electrostatics, protein design

52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2014 Frankaer CG, Moroz OV, Turkenburg JP, Aspmo SI, Thymark M, Friis EP, Stahl K, Nielsen JE, Wilson KS, Harris P. Analysis of an industrial production suspension of Bacillus lentus subtilisin crystals by powder diffraction: a powerful quality-control tool. Acta Crystallographica. Section D, Biological Crystallography. 70: 1115-23. PMID 24699655 DOI: 10.1107/S1399004714001497  0.96
2013 Kukic P, Farrell D, McIntosh LP, García-Moreno E B, Jensen KS, Toleikis Z, Teilum K, Nielsen JE. Protein dielectric constants determined from NMR chemical shift perturbations. Journal of the American Chemical Society. 135: 16968-76. PMID 24124752 DOI: 10.1021/ja406995j  0.96
2013 Ludwiczek ML, D'Angelo I, Yalloway GN, Brockerman JA, Okon M, Nielsen JE, Strynadka NC, Withers SG, McIntosh LP. Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase. Biochemistry. 52: 3138-56. PMID 23578322 DOI: 10.1021/bi400034m  0.96
2012 Farrell D, Nielsen JE. DataPipeline: automated importing and fitting of large amounts of biophysical data. Journal of Computational Chemistry. 33: 2357-62. PMID 22806579 DOI: 10.1002/jcc.23066  0.96
2012 Farrell D, Webb H, Johnston MA, Poulsen TA, O'Meara F, Christensen LL, Beier L, Borchert TV, Nielsen JE. Toward fast determination of protein stability maps: experimental and theoretical analysis of mutants of a Nocardiopsis prasina serine protease. Biochemistry. 51: 5339-47. PMID 22668005 DOI: 10.1021/bi201926f  0.96
2012 Bradley J, O'Meara F, Farrell D, Nielsen JE. Highly perturbed pKa values in the unfolded state of hen egg white lysozyme. Biophysical Journal. 102: 1636-45. PMID 22500764 DOI: 10.1016/j.bpj.2012.02.048  0.96
2012 Johnston MA, Farrell D, Nielsen JE. A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. Journal of Computer-Aided Molecular Design. 26: 387-96. PMID 22476577 DOI: 10.1007/s10822-012-9564-z  0.96
2012 Bjarnadottir U, Nielsen JE. Predicting the open conformations of protein kinases using molecular dynamics simulations. Biopolymers. 97: 65-72. PMID 21858778 DOI: 10.1002/bip.21704  0.96
2011 Nielsen JE, Gunner MR, García-Moreno BE. The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins. 79: 3249-59. PMID 22002877 DOI: 10.1002/prot.23194  0.96
2011 McIntosh LP, Naito D, Baturin SJ, Okon M, Joshi MD, Nielsen JE. Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations. Journal of Biomolecular Nmr. 51: 5-19. PMID 21947911 DOI: 10.1007/s10858-011-9537-x  0.96
2011 Casey J, Kawaguchi R, Morrissey M, Sun H, McGettigan P, Nielsen JE, Conroy J, Regan R, Kenny E, Cormican P, Morris DW, Tormey P, Chróinín MN, Kennedy BN, Lynch S, et al. First implication of STRA6 mutations in isolated anophthalmia, microphthalmia, and coloboma: a new dimension to the STRA6 phenotype. Human Mutation. 32: 1417-26. PMID 21901792 DOI: 10.1002/humu.21590  0.96
2011 Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE. On the development of protein pKa calculation algorithms. Proteins. 79: 3287-98. PMID 21744393 DOI: 10.1002/prot.23091  0.96
2011 Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, Li WW, Nielsen JE, Baker NA. Web servers and services for electrostatics calculations with APBS and PDB2PQR. Journal of Computational Chemistry. 32: 1488-91. PMID 21425296 DOI: 10.1002/jcc.21720  0.96
2011 Alendé N, Nielsen JE, Shields DC, Khaldi N. Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution. Proteins. 79: 1635-48. PMID 21387414 DOI: 10.1002/prot.22990  0.96
2011 Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Søndergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE. Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations. Proteins. 79: 685-702. PMID 21287606 DOI: 10.1002/prot.22886  0.96
2011 Johnston MA, Søndergaard CR, Nielsen JE. Integrated prediction of the effect of mutations on multiple protein characteristics. Proteins. 79: 165-78. PMID 21058401 DOI: 10.1002/prot.22870  0.96
2011 Czodrowski P, Søndergaard CR, Dohm S, Klebe G, Nielsen JE. LigpKa-a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations Journal of Cheminformatics. 3. DOI: 10.1186/1758-2946-3-S1-P21  0.96
2010 Kuki? P, Nielsen JE. Electrostatics in proteins and protein-ligand complexes. Future Medicinal Chemistry. 2: 647-66. PMID 21426012 DOI: 10.4155/fmc.10.6  0.96
2010 Bjarnadottir U, Nielsen JE. Calculating pKa values in the cAMP-dependent protein kinase: the effect of conformational change and ligand binding. Protein Science : a Publication of the Protein Society. 19: 2485-97. PMID 20954248 DOI: 10.1002/pro.530  0.96
2010 Farrell D, O'Meara F, Johnston M, Bradley J, Søndergaard CR, Georgi N, Webb H, Tynan-Connolly BM, Bjarnadottir U, Carstensen T, Nielsen JE. Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies. Nucleic Acids Research. 38: e186. PMID 20724439 DOI: 10.1093/nar/gkq726  0.96
2010 Higgins WJ, Fox DM, Kowalski PS, Nielsen JE, Worrall DM. Heparin enhances serpin inhibition of the cysteine protease cathepsin L. The Journal of Biological Chemistry. 285: 3722-9. PMID 19959474 DOI: 10.1074/jbc.M109.037358  0.96
2010 Farrell D, Miranda ES, Webb H, Georgi N, Crowley PB, McIntosh LP, Nielsen JE. Titration DB: Storage and analysis of NMR-monitored protein pH titration curves Proteins: Structure, Function and Bioinformatics. 78: 843-857. PMID 19899070 DOI: 10.1002/prot.22611  0.96
2010 Kuki? P, Farrell D, Søndergaard CR, Bjarnadottir U, Bradley J, Pollastri G, Nielsen JE. Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift. Proteins. 78: 971-84. PMID 19894279 DOI: 10.1002/prot.22621  0.96
2009 Søndergaard CR, Garrett AE, Carstensen T, Pollastri G, Nielsen JE. Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions. Journal of Medicinal Chemistry. 52: 5673-84. PMID 19711919 DOI: 10.1021/jm8016464  0.96
2009 Reitinger S, Müllegger J, Greiderer B, Nielsen JE, Lepperdinger G. Designed human serum hyaluronidase 1 variant, HYAL1ΔL, exhibits activity up to pH 5.9 Journal of Biological Chemistry. 284: 19173-19177. PMID 19478093 DOI: 10.1074/jbc.C109.004358  0.96
2009 Nielsen JE. Chapter 9 Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting Methods in Enzymology. 454: 233-258. PMID 19216929 DOI: 10.1016/S0076-6879(08)03809-3  0.96
2008 Søndergaard CR, McIntosh LP, Pollastri G, Nielsen JE. Determination of electrostatic interaction energies and protonation state populations in enzyme active sites. Journal of Molecular Biology. 376: 269-87. PMID 18155242 DOI: 10.1016/j.jmb.2007.09.070  0.96
2008 Nielsen JE. Chapter 5 Analyzing Protein NMR pH-Titration Curves Annual Reports in Computational Chemistry. 4: 89-106. DOI: 10.1016/S1574-1400(08)00005-4  0.96
2007 Schubert M, Poon DK, Wicki J, Tarling CA, Kwan EM, Nielsen JE, Withers SG, McIntosh LP. Probing electrostatic interactions along the reaction pathway of a glycoside hydrolase: histidine characterization by NMR spectroscopy. Biochemistry. 46: 7383-95. PMID 17547373 DOI: 10.1021/bi700249m  0.96
2007 Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Research. 35: W522-5. PMID 17488841 DOI: 10.1093/nar/gkm276  0.96
2007 Tynan-Connolly BM, Nielsen JE. Redesigning protein pKa values Protein Science. 16: 239-249. PMID 17189477 DOI: 10.1110/ps.062538707  0.96
2007 Nielsen JE. Analysing the pH-dependent properties of proteins using pKa calculations Journal of Molecular Graphics and Modelling. 25: 691-699. PMID 16815056 DOI: 10.1016/j.jmgm.2006.05.007  0.96
2006 Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA. Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Modeling & Simulation : a Siam Interdisciplinary Journal. 5: 1196-1213. PMID 18841247 DOI: 10.1137/050647670  0.96
2006 Cummins EP, Berra E, Comerford KM, Ginouves A, Fitzgerald KT, Seeballuck F, Godson C, Nielsen JE, Moynagh P, Pouyssegur J, Taylor CT. Prolyl hydroxylase-1 negatively regulates IkappaB kinase-beta, giving insight into hypoxia-induced NFkappaB activity. Proceedings of the National Academy of Sciences of the United States of America. 103: 18154-9. PMID 17114296 DOI: 10.1073/pnas.0602235103  0.96
2006 Tynan-Connolly BM, Nielsen JE. pKD: Re-designing protein pKa values Nucleic Acids Research. 34: W48-W51. PMID 16845054 DOI: 10.1093/nar/gkl192  0.96
2006 Damen E, Krieger E, Nielsen JE, Eygensteyn J, van Leeuwen JE. The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide. The Biochemical Journal. 398: 399-409. PMID 16737443 DOI: 10.1042/BJ20060033  0.96
2006 Krieger E, Nielsen JE, Spronk CA, Vriend G. Fast empirical pKa prediction by Ewald summation. Journal of Molecular Graphics & Modelling. 25: 481-6. PMID 16644253 DOI: 10.1016/j.jmgm.2006.02.009  0.96
2005 Tolbert BS, Tajc SG, Webb H, Snyder J, Nielsen JE, Miller BL, Basavappa R. The active site cysteine of ubiquitin-conjugating enzymes has a significantly elevated pKa: functional implications. Biochemistry. 44: 16385-91. PMID 16342931 DOI: 10.1021/bi0514459  0.96
2004 Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research. 32: W665-7. PMID 15215472 DOI: 10.1093/nar/gkh381  1
2004 Synstad B, Gåseidnes S, Van Aalten DM, Vriend G, Nielsen JE, Eijsink VG. Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase. European Journal of Biochemistry / Febs. 271: 253-62. PMID 14717693 DOI: 10.1046/j.1432-1033.2003.03923.x  0.96
2003 Nielsen JE, McCammon JA. Calculating pKa values in enzyme active sites. Protein Science : a Publication of the Protein Society. 12: 1894-901. PMID 12930989 DOI: 10.1110/ps.03114903  1
2003 Nielsen JE, McCammon JA. On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Science : a Publication of the Protein Society. 12: 313-26. PMID 12538895 DOI: 10.1110/ps.0229903  1
2003 GÃ¥seidnes S, Synstad B, Nielsen JE, Eijsink VGH. Rational engineering of the stability and the catalytic performance of enzymes Journal of Molecular Catalysis B: Enzymatic. 21: 3-8. DOI: 10.1016/S1381-1177(02)00136-4  0.96
2002 Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. Journal of Molecular Biology. 320: 369-87. PMID 12079393 DOI: 10.1016/S0022-2836(02)00442-4  0.96
2002 de Kreij A, van den Burg B, Venema G, Vriend G, Eijsink VG, Nielsen JE. The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease. The Journal of Biological Chemistry. 277: 15432-8. PMID 11859085 DOI: 10.1074/jbc.M200807200  0.96
2001 Nielsen JE, Borchert TV, Vriend G. The determinants of alpha-amylase pH-activity profiles. Protein Engineering. 14: 505-12. PMID 11522925  0.96
2001 Joshi MD, Sidhu G, Nielsen JE, Brayer GD, Withers SG, McIntosh LP. Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase Biochemistry. 40: 10115-10139. PMID 11513590 DOI: 10.1021/bi0105429  0.96
2001 Nielsen JE, Vriend G. Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. Proteins. 43: 403-12. PMID 11340657 DOI: 10.1002/prot.1053  0.96
2000 Nielsen JE, Borchert TV. Protein engineering of bacterial α-amylases Biochimica Et Biophysica Acta - Protein Structure and Molecular Enzymology. 1543: 253-274. PMID 11150610 DOI: 10.1016/S0167-4838(00)00240-5  0.96
2000 Lambeir AM, Backmann J, Ruiz-Sanz J, Filimonov V, Nielsen JE, Kursula I, Norledge BV, Wierenga RK. The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. European Journal of Biochemistry / Febs. 267: 2516-24. PMID 10785370 DOI: 10.1046/j.1432-1327.2000.01254.x  0.96
1999 Nielsen JE, Beier L, Otzen D, Borchert TV, Frantzen HB, Andersen KV, Svendsen A. Electrostatics in the active site of an α-amylase European Journal of Biochemistry. 264: 816-824. PMID 10491128 DOI: 10.1046/j.1432-1327.1999.00664.x  0.96
1999 Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC. Improving macromolecular electrostatics calculations. Protein Engineering. 12: 657-62. PMID 10469826  0.96
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