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Patrik Rydberg · SciRah

Researcher profile · Semantic Scholar

Patrik Rydberg

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Patrik Rydberg — researcher profile on SciRah

h-index: 26
Works: 49
Citations: 2,097

Most-cited papers

SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism.
Patrik Rydberg, D. Gloriam, Jed Zaretzki, C. Breneman +1 more
2010ACS Medicinal Chemistry Letters292 citations Open access
Semantic Scholar
On the role of the axial ligand in heme proteins: a theoretical study
Patrik Rydberg, Emma Sigfridsson, U. Ryde
2004JBIC Journal of Biological Inorganic Chemistry155 citations
Semantic Scholar
Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.
H. Hersleth, U. Ryde, Patrik Rydberg, C. Görbitz +1 more
2006Journal of Inorganic Biochemistry143 citations
Semantic Scholar
The SMARTCyp cytochrome P450 metabolism prediction server
Patrik Rydberg, D. Gloriam, L. Olsen
2010Bioinform.126 citations Open access
Semantic Scholar
Prediction of activation energies for hydrogen abstraction by cytochrome p450.
L. Olsen, Patrik Rydberg, T. Rod, U. Ryde
2006Journal of Medicinal Chemistry113 citations Open access
Semantic Scholar
RS-Predictor: A new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4
Jed Zaretzki, Charles Bergeron, Patrik Rydberg, Tao-wei Huang +2 more
2011Journal of Chemical Information and Modeling91 citations Open access
Semantic Scholar
RS-Predictor models augmented with SMARTCyp reactivities: Robust metabolic regioselectivity predictions for nine CYP isozymes
Jed Zaretzki, Patrik Rydberg, Charles Bergeron, Kristin P. Bennett +2 more
2012Journal of Chemical Information and Modeling76 citations Open access
Semantic Scholar
Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450.
Patrik Rydberg, U. Ryde, L. Olsen
2008Journal of Chemical Theory and Computation76 citations Open access
Semantic Scholar
WhichCyp: prediction of cytochromes P450 inhibition
M. Rostkowski, O. Spjuth, Patrik Rydberg
2013Bioinform.68 citations Open access
Semantic Scholar
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules
Jed Zaretzki, Charles Bergeron, Tao-wei Huang, Patrik Rydberg +2 more
2013Bioinform.64 citations Open access
Semantic Scholar
The accuracy of geometries for iron porphyrin complexes from density functional theory.
Patrik Rydberg, L. Olsen
2009Journal of Physical Chemistry A58 citations
Semantic Scholar
FAst MEtabolizer (FAME): A Rapid and Accurate Predictor of Sites of Metabolism in Multiple Species by Endogenous Enzymes
J. Kirchmair, M. Williamson, Avid M. Afzal, Jonathan D. Tyzack +4 more
2013Journal of Chemical Information and Modeling54 citations
Semantic Scholar
General Transition-State Force Field for Cytochrome P450 Hydroxylation.
Patrik Rydberg, L. Olsen, Per-Ola Norrby, U. Ryde
2007Journal of Chemical Theory and Computation54 citations Open access
Semantic Scholar
Predicting Drug Metabolism by Cytochrome P450 2C9: Comparison with the 2D6 and 3A4 Isoforms
Patrik Rydberg, L. Olsen
2012ChemMedChem53 citations
Semantic Scholar
Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
P. Mikulskis, S. Genheden, Patrik Rydberg, L. Sandberg +2 more
2012Journal of Computer-Aided Molecular Design52 citations Open access
Semantic Scholar
Prediction of activation energies for aromatic oxidation by cytochrome P450.
Patrik Rydberg, U. Ryde, L. Olsen
2008Journal of Physical Chemistry A51 citations Open access
Semantic Scholar
Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6.
Patrik Rydberg, L. Olsen
2012ACS Medicinal Chemistry Letters49 citations Open access
Semantic Scholar
Fast Prediction of Cytochrome P450 Mediated Drug Metabolism
Patrik Rydberg, P. Vasanthanathan, C. Oostenbrink, L. Olsen
2009ChemMedChem48 citations Open access
Semantic Scholar
The contribution of atom accessibility to site of metabolism models for cytochromes P450.
Patrik Rydberg, M. Rostkowski, D. Gloriam, L. Olsen
2013Molecular Pharmaceutics42 citations
Semantic Scholar
Dynamics of water molecules in the active-site cavity of human cytochromes P450.
Patrik Rydberg, T. Rod, L. Olsen, U. Ryde
2007Journal of Physical Chemistry B42 citations Open access
Semantic Scholar
Mechanism of the N-hydroxylation of primary and secondary amines by cytochrome P450.
S. T. Seger, Patrik Rydberg, L. Olsen
2015Chemical Research in Toxicology38 citations
Semantic Scholar
Structural model and trans-interaction of the entire ectodomain of the olfactory cell adhesion molecule.
N. Kulahin, O. Kristensen, K. K. Rasmussen, L. Olsen +7 more
2011Structure34 citations Open access
Semantic Scholar
Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2.
R. Lonsdale, Rachel M. Fort, Patrik Rydberg, J. Harvey +1 more
2016Chemical Research in Toxicology30 citations Open access
Semantic Scholar
Do Two Different Reaction Mechanisms Contribute to the Hydroxylation of Primary Amines by Cytochrome P450?
Patrik Rydberg, L. Olsen
2011Journal of Chemical Theory and Computation28 citations
Semantic Scholar
Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.
Patrik Rydberg, Sine Myrup Hansen, J. Kongsted, Per-Ola Norrby +2 more
2008Journal of Chemical Theory and Computation28 citations Open access
Semantic Scholar
Protonation of the proximal histidine ligand in heme peroxidases.
J. Heimdal, Patrik Rydberg, U. Ryde
2008Journal of Physical Chemistry B27 citations Open access
Semantic Scholar
Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions.
Patrik Rydberg, R. Lonsdale, J. Harvey, A. Mulholland +1 more
2014Journal of Molecular Graphics and Modelling24 citations
Semantic Scholar
Application of Q2MM to Stereoselective Reactions
S. O. N. Lill, A. Forbes, Patrick J. Donoghue, Vincenzo Verdolino +3 more
201023 citations
Semantic Scholar
Use of density functional theory in drug metabolism studies
Patrik Rydberg, F. Jørgensen, L. Olsen
2014Expert Opinion on Drug Metabolism & Toxicology22 citations
Semantic Scholar
Nitrogen inversion barriers affect the N-oxidation of tertiary alkylamines by cytochromes P450.
Patrik Rydberg, Martin S. Jørgensen, T. Jacobsen, Anne-Marie Jacobsen +2 more
2013Angewandte Chemie22 citations
Semantic Scholar
Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase.
T. Rod, Patrik Rydberg, U. Ryde
2006Journal of Chemical Physics21 citations Open access
Semantic Scholar
Quantum-mechanical studies of reactions performed by cytochrome P450 enzymes
Patrik Rydberg, L. Olsen, U. Ryde
201216 citations Open access
Semantic Scholar
A comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin.
E. Ryabova, Patrik Rydberg, M. Kolberg, Espen Harbitz +4 more
2005Journal of Inorganic Biochemistry16 citations
Semantic Scholar
XMetDB: an open access database for xenobiotic metabolism
O. Spjuth, Patrik Rydberg, Egon Willighagen, C. Evelo +1 more
2016Journal of Cheminformatics15 citations Open access
Semantic Scholar
Branched nanotrees with immobilized acetylcholine esterase for nanobiosensor applications
K. Risveden, K. Dick, S. Bhand, Patrik Rydberg +2 more
2010Nanotechnology11 citations Open access
Semantic Scholar
Theoretical Study of the Cytochrome P450 Mediated Metabolism of Phosphorodithioate Pesticides.
Patrik Rydberg
2012Journal of Chemical Theory and Computation9 citations
Semantic Scholar
Density Functional Theory Study on the Formation of Reactive Benzoquinone Imines by Hydrogen Abstraction
Rasmus Leth, Patrik Rydberg, F. Jørgensen, L. Olsen
2015Journal of Chemical Information and Modeling7 citations
Semantic Scholar
Prediction of cytochrome p450 mediated metabolism of designer drugs.
L. M. Nielsen, K. Linnet, L. Olsen, Patrik Rydberg
2014Current Topics in Medicinal Chemistry6 citations
Semantic Scholar
Reactivity‐Based Approaches and Machine Learning Methods for Predicting the Sites of Cytochrome P450‐Mediated Metabolism
Patrik Rydberg
20144 citations
Semantic Scholar
Enrichment of True Positives from Structural Alerts Through the Use of Novel Atomic Fragment Based Descriptors
A. Long, Patrik Rydberg
2013Molecular Informatics3 citations
Semantic Scholar
Tool Wear Compensation
E. Larsson, David Eriksson, Patrik Rydberg
20093 citations
Semantic Scholar
Quantum-mechanical studies of reactions performed by cytochrome P 450 enzymes
Patrik Rydberg, L. Olsen, Ulf Rydeb
20132 citations
Semantic Scholar
Structure-Activity Relationships and Identification of Optmized CC-Chemokine Receptor CCR1, 5, and 8 Metal-Ion Chelators
A.P.A. Chalikiopoulos, S. Thiele, Mikkel Malmgaard-Clausen, Patrik Rydberg +5 more
2013Journal of Chemical Information and Modeling2 citations
Semantic Scholar
Comment on “binding free energies of inhibitors to iron porphyrin complex as a model for cytochrome p450”
Patrik Rydberg
2012Biopolymers2 citations
Semantic Scholar
A comparison of the tetrapyrrole cofactors in nature and their tuning by axial ligands
Kasper P. Jensen, Patrik Rydberg, J. Heimdal, U. Ryde
20082 citations Open access
Semantic Scholar
On the role of the axial ligand in haem proteins – a theoretical study
Patrik Rydberg, Emma Sigfridsson, U. Ryde
20170 citations
Semantic Scholar
Application of Q 2 MM to stereoselective reactions
S. O. N. Lill, A. Forbes, Patrick J. Donoghue, Vincenzo Verdolino +3 more
20100 citations
Semantic Scholar
Theoretical Studies of Cytochrome P450
Patrik Rydberg
20070 citations
Semantic Scholar
2016). Quantum mechanics/molecular mechanics modeling of drug metabolism: Mexiletine N-hydroxylation by cytochrome P450 1A2. Chemical Research in Toxicology, 29(6), 963-971.
R. Lonsdale, Rachel M. Fort, Patrik Rydberg, J. N. Harvey +1 more
0 citations
Semantic Scholar

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L. Olsen×25
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U. Ryde×15
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D. Gloriam×4
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Jed Zaretzki×4
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Per-Ola Norrby×4

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