Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Chresten R, Søndergaard"'
Publikováno v:
Journal of Chemical Theory and Computation; Vol 7
The new empirical rules for protein pKa predictions implemented in the PROPKA3.0 software package (Olsson et al. J. Chem. Theory Comput.2010, 7, 525-537) have been extended to the prediction of pKa shifts of active site residues and ionizable ligand
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8c52feeb91e46163bbfd10dcc438dcce
https://doi.org/10.1021/ct200133y
https://doi.org/10.1021/ct200133y
Publikováno v:
Journal of Chemical Theory and Computation. 7:525-537
In this study, we have revised the rules and parameters for one of the most commonly used empirical pKa predictors, PROPKA, based on better physical description of the desolvation and dielectric response for the protein. We have introduced a new and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::13ead73c7e92d5b3ee27af9efaf8099c
https://doi.org/10.1021/ct100578z
https://doi.org/10.1021/ct100578z
Autor:
Gregory M. Lee, Kaare Teilum, Jens Erik Nielsen, Helen Webb, Lawrence P. McIntosh, Chandralal M. Hewage, Fergal O'Meara, Damien Farrell, Barbara Mary Tynan-Connolly, Chresten R. Søndergaard
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 79:685-702
Site-specific pKa values measured by NMR spectroscopy provide essential information on protein electrostatics, the pH-dependence of protein structure, dynamics and function, and constitute an important benchmark for protein pKa calculation algorithms
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::691e6215c6b3f46236738c835e4c53eb
https://doi.org/10.1002/prot.22886
https://doi.org/10.1002/prot.22886
Autor:
Damien Farrell, Gianluca Pollastri, John F. Bradley, Chresten R. Søndergaard, Predrag Kukic, Jens Erik Nielsen, Una Bjarnadottir
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 78:971-984
pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural tra
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d05d73dd2cf27099dfbee4d16bd58746
https://doi.org/10.1002/prot.22621
https://doi.org/10.1002/prot.22621
Autor:
Jens Erik Nielsen, Gianluca Pollastri, Alison Elizabeth Garrett, Chresten R. Søndergaard, Tommy Carstensen
Publikováno v:
Journal of Medicinal Chemistry. 52:5673-5684
The development of docking scoring functions requires high-resolution 3D structures of protein-ligand complexes for which the binding affinity of the ligand has been measured experimentally. Protein-ligand binding affinities are measured in solution
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f0f30d313c425a87879c2231758acc1
https://doi.org/10.1021/jm8016464
https://doi.org/10.1021/jm8016464
Publikováno v:
Journal of Cheminformatics, Vol 3, Iss Suppl 1, p P21 (2011)
Journal of Cheminformatics
Journal of Cheminformatics
Electrostatic forces play a large role in determining the strength of protein-ligand interactions, and the calculation of pKa value shifts upon ligand binding is therefore an important component of any accurate protein-ligand binding calculation. How
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cb2806a880a520118749f36b3f33dad8
https://doaj.org/article/c8792e123a244b5ab6f0d698da241ebf
https://doaj.org/article/c8792e123a244b5ab6f0d698da241ebf
Publikováno v:
BMC Structural Biology, Vol 11, Iss 1, p 6 (2011)
BMC Structural Biology
BMC Structural Biology
Background Charge states of ionizable residues in proteins determine their pH-dependent properties through their pKa values. Thus, various theoretical methods to determine ionization constants of residues in biological systems have been developed. On
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f6e6463885fbfe6a684c4ee4b1ec181e
https://doi.org/10.1186/1472-6807-11-6
https://doi.org/10.1186/1472-6807-11-6
Autor:
Predrag, Kukić, Damien, Farrell, Chresten R, Søndergaard, Una, Bjarnadottir, John, Bradley, Gianluca, Pollastri, Jens Erik, Nielsen
Publikováno v:
Proteins. 78(4)
pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural tra
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::7e803ce0311231f8277750fe4c5dd16d
https://pubmed.ncbi.nlm.nih.gov/19894279
https://pubmed.ncbi.nlm.nih.gov/19894279
Publikováno v:
Journal of molecular biology. 376(1)
The pH-dependence of the NMR chemical shift for titratable groups in proteins often deviate from a standard Henderson-Hasselbalch (HH) titration curve. A non-HH dependence of the chemical shift for a given residue can arise from a single-site, non-HH
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::71501fffc2add704815da5c54b9499f1
https://pubmed.ncbi.nlm.nih.gov/18155242
https://pubmed.ncbi.nlm.nih.gov/18155242
Autor:
Salyha Ali, Susana C. M. Teixeira, Chresten R. Søndergaard, Matthew P. Blakeley, E. Pellegrini, Richard W. Pickersgill
Publikováno v:
Acta Crystallographica Section A Foundations of Crystallography. 67:C734-C734
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::cc9b8d9ddf4be85d805482dc704d51a2
https://doi.org/10.1107/s0108767311081487
https://doi.org/10.1107/s0108767311081487