| Year |
Citation |
Score |
| 2018 |
Jensen PF, Kadziola A, Comamala G, Segura DR, Anderson L, Poulsen JN, Rasmussen KK, Agarwal S, Sainathan RK, Monrad RN, Svendsen A, Nielsen JE, Lo Leggio L, Rand KD. Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity. Cell Chemical Biology. PMID 30503284 DOI: 10.1016/J.Chembiol.2018.10.016 |
0.322 |
|
| 2017 |
Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, ... ... Nielsen JE, et al. Improvements to the APBS biomolecular solvation software suite. Protein Science : a Publication of the Protein Society. PMID 28836357 DOI: 10.1002/Pro.3280 |
0.604 |
|
| 2017 |
Meekrathok P, Kukic P, Nielsen JE, Suginta W. Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations. Journal of Chemical Information and Modeling. PMID 28230366 DOI: 10.1021/Acs.Jcim.6B00536 |
0.309 |
|
| 2015 |
Kayikci Ö, Nielsen J. Glucose repression in Saccharomyces cerevisiae. Fems Yeast Research. 15. PMID 26205245 DOI: 10.1093/Femsyr/Fov068 |
0.675 |
|
| 2013 |
Kukic P, Farrell D, McIntosh LP, GarcÃa-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 |
0.34 |
|
| 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 |
0.35 |
|
| 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 |
0.376 |
|
| 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 |
0.305 |
|
| 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 |
0.34 |
|
| 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 |
0.311 |
|
| 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 |
0.382 |
|
| 2011 |
Alexov E, Mehler EL, Baker N, Baptista AM, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MH, Shen JK, Warwicker J, Williams S, Word JM. Progress in the prediction of pKa values in proteins. Proteins. 79: 3260-75. PMID 22002859 DOI: 10.1002/Prot.23189 |
0.573 |
|
| 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 |
0.35 |
|
| 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 |
0.577 |
|
| 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 |
0.536 |
|
| 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 |
0.322 |
|
| 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 |
0.37 |
|
| 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 |
0.367 |
|
| 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 |
0.339 |
|
| 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 |
0.333 |
|
| 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 |
0.345 |
|
| 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 |
0.348 |
|
| 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 |
0.36 |
|
| 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 |
0.316 |
|
| 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 |
0.326 |
|
| 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 |
0.381 |
|
| 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 |
0.375 |
|
| 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 |
0.344 |
|
| 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 |
0.349 |
|
| 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 |
0.588 |
|
| 2007 |
Tynan-Connolly BM, Nielsen JE. Redesigning protein pKa values Protein Science. 16: 239-249. PMID 17189477 DOI: 10.1110/Ps.062538707 |
0.36 |
|
| 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 |
0.39 |
|
| 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 |
0.539 |
|
| 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 |
0.372 |
|
| 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 |
0.33 |
|
| 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 |
0.554 |
|
| 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 |
0.332 |
|
| 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 |
0.625 |
|
| 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 |
0.545 |
|
| 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 |
0.507 |
|
| 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 |
0.471 |
|
| 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 |
0.516 |
|
| 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 |
0.526 |
|
| 2001 |
Nielsen JE, Borchert TV, Vriend G. The determinants of alpha-amylase pH-activity profiles. Protein Engineering. 14: 505-12. PMID 11522925 DOI: 10.1093/Protein/14.7.505 |
0.539 |
|
| 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: 10.2210/Pdb1Hv0/Pdb |
0.369 |
|
| 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 |
0.546 |
|
| 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 |
0.36 |
|
| 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 |
0.353 |
|
| 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 DOI: 10.1093/Protein/12.8.657 |
0.645 |
|
| Show low-probability matches. |