Patrik Rydberg
Patrik Rydberg
Associate Director, Computational Chemmistry, Optibrium Ltd.
Verified email at - Homepage
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SMARTCyp: a 2D method for prediction of cytochrome P450-mediated drug metabolism
P Rydberg, DE Gloriam, J Zaretzki, C Breneman, L Olsen
ACS medicinal chemistry letters 1 (3), 96-100, 2010
On the role of the axial ligand in heme proteins: a theoretical study
P Rydberg, E Sigfridsson, U Ryde
JBIC Journal of Biological Inorganic Chemistry 9, 203-223, 2004
Structures of the high-valent metal-ion haem–oxygen intermediates in peroxidases, oxygenases and catalases
HP Hersleth, U Ryde, P Rydberg, CH G÷rbitz, KK Andersson
Journal of inorganic biochemistry 100 (4), 460-476, 2006
The SMARTCyp cytochrome P450 metabolism prediction server
P Rydberg, DE Gloriam, L Olsen
Bioinformatics 26 (23), 2988-2989, 2010
Prediction of activation energies for hydrogen abstraction by cytochrome P450
L Olsen, P Rydberg, TH Rod, U Ryde
Journal of medicinal chemistry 49 (22), 6489-6499, 2006
RS-predictor: a new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4
J Zaretzki, C Bergeron, P Rydberg, T Huang, KP Bennett, CM Breneman
Journal of chemical information and modeling 51 (7), 1667-1689, 2011
Sulfoxide, sulfur, and nitrogen oxidation and dealkylation by cytochrome P450
P Rydberg, U Ryde, L Olsen
Journal of chemical theory and computation 4 (8), 1369-1377, 2008
RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes
J Zaretzki, P Rydberg, C Bergeron, KP Bennett, L Olsen, CM Breneman
Journal of chemical information and modeling 52 (6), 1637-1659, 2012
WhichCyp: prediction of cytochromes P450 inhibition
M Rostkowski, O Spjuth, P Rydberg
Bioinformatics 29 (16), 2051-2052, 2013
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules
J Zaretzki, C Bergeron, T Huang, P Rydberg, SJ Swamidass, ...
Bioinformatics 29 (4), 497-498, 2013
Predicting drug metabolism by cytochrome P450 2C9: comparison with the 2D6 and 3A4 isoforms
P Rydberg, L Olsen
ChemMedChem 7 (7), 1202-1209, 2012
FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes
J Kirchmair, MJ Williamson, AM Afzal, JD Tyzack, APK Choy, A Howlett, ...
Journal of chemical information and modeling 53 (11), 2896-2907, 2013
The accuracy of geometries for iron porphyrin complexes from density functional theory
P Rydberg, L Olsen
The Journal of Physical Chemistry A 113 (43), 11949-11953, 2009
General transition-state force field for cytochrome P450 hydroxylation
P Rydberg, L Olsen, PO Norrby, U Ryde
Journal of Chemical Theory and Computation 3 (5), 1765-1773, 2007
Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
P Mikulskis, S Genheden, P Rydberg, L Sandberg, L Olsen, U Ryde
Journal of computer-aided molecular design 26, 527-541, 2012
Prediction of activation energies for aromatic oxidation by cytochrome P450
P Rydberg, U Ryde, L Olsen
The journal of physical chemistry A 112 (50), 13058-13065, 2008
Fast prediction of cytochrome P450 mediated drug metabolism
P Rydberg, P Vasanthanathan, C Oostenbrink, L Olsen
ChemMedChem 4 (12), 2070-2079, 2009
Ligand-based Site of Metabolism Prediction for Cytochrome P450 2D6
P Rydberg, L Olsen
ACS Medicinal Chemistry Letters 3 (1), 69-73, 2012
Dynamics of water molecules in the active-site cavity of human cytochromes P450
P Rydberg, TH Rod, L Olsen, U Ryde
The Journal of Physical Chemistry B 111 (19), 5445-5457, 2007
The contribution of atom accessibility to site of metabolism models for cytochromes P450
P Rydberg, M Rostkowski, DE Gloriam, L Olsen
Molecular pharmaceutics 10 (4), 1216-1223, 2013
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