List of works - Patrik Rydberg

SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism

scientific article (publication date: 10 June 2010)

The SMARTCyp cytochrome P450 metabolism prediction server

scientific article

On the role of the axial ligand in heme proteins: a theoretical study.

scientific article

Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.

scientific article

Prediction of activation energies for hydrogen abstraction by cytochrome p450.

scientific article published in November 2006

RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes

scientific article

RS-predictor: a new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4.

scientific article published on 15 June 2011

Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6.

scientific article

Dynamics of Water Molecules in the Active-Site Cavity of Human Cytochromes P450

article

Structural model and trans-interaction of the entire ectodomain of the olfactory cell adhesion molecule

scientific article

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

Predicting drug metabolism by cytochrome P450 2C9: comparison with the 2D6 and 3A4 isoforms

scientific article

Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450

scientific article published on 01 August 2008

Prediction of activation energies for aromatic oxidation by cytochrome P450.

scientific article

WhichCyp: prediction of cytochromes P450 inhibition

scientific article

FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes

scientific article published on 12 November 2013

The Accuracy of Geometries for Iron Porphyrin Complexes from Density Functional Theory†

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

article

RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules.

scientific article published on 14 December 2012

The contribution of atom accessibility to site of metabolism models for cytochromes P450.

scientific article published on 22 January 2013

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

scientific article published on 01 May 2006

Do Two Different Reaction Mechanisms Contribute to the Hydroxylation of Primary Amines by Cytochrome P450?

Use of density functional theory in drug metabolism studies.

scientific article published on 03 December 2013

Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.

scientific article

General Transition-State Force Field for Cytochrome P450 Hydroxylation

scientific article published on 01 September 2007

XMetDB: an open access database for xenobiotic metabolism

scientific article

Protonation of the proximal histidine ligand in heme peroxidases

scientific article published on 6 February 2008

Nitrogen inversion barriers affect the N-oxidation of tertiary alkylamines by cytochromes P450.

scientific article

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2

scientific article published on 10 May 2016

Mechanism of the N-Hydroxylation of Primary and Secondary Amines by Cytochrome P450

Theoretical Study of the Cytochrome P450 Mediated Metabolism of Phosphorodithioate Pesticides

scientific article published on July 20, 2012

Branched nanotrees with immobilized acetylcholine esterase for nanobiosensor applications

scientific article published on 21 December 2009

Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions

scientific article published on 23 June 2014

Structure-activity relationships and identification of optmized CC-chemokine receptor CCR1, 5, and 8 metal-ion chelators

scientific article published on 22 October 2013

A comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin

scientific article published in March 2005

Comment on “binding free energies of inhibitors to iron porphyrin complex as a model for cytochrome p450”

article

Prediction of Cytochrome P450 Mediated Metabolism of Designer Drugs

scientific article published on 01 January 2014

Density functional theory study on the formation of reactive benzoquinone imines by hydrogen abstraction.

scientific article

Enrichment of True Positives from Structural Alerts Through the Use of Novel Atomic Fragment Based Descriptors

scientific article published on 11 January 2013

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

scholarly article by Patrik Rydberg et al published 30 November 2009 in ChemMedChem

List of works by Patrik Rydberg

SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism

The SMARTCyp cytochrome P450 metabolism prediction server

On the role of the axial ligand in heme proteins: a theoretical study.

Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.

Prediction of activation energies for hydrogen abstraction by cytochrome p450.

RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes

RS-predictor: a new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4.

Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6.

Dynamics of Water Molecules in the Active-Site Cavity of Human Cytochromes P450

Structural model and trans-interaction of the entire ectodomain of the olfactory cell adhesion molecule

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

Predicting drug metabolism by cytochrome P450 2C9: comparison with the 2D6 and 3A4 isoforms

Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450

Prediction of activation energies for aromatic oxidation by cytochrome P450.

WhichCyp: prediction of cytochromes P450 inhibition

FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes

The Accuracy of Geometries for Iron Porphyrin Complexes from Density Functional Theory†

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules.

The contribution of atom accessibility to site of metabolism models for cytochromes P450.

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

Do Two Different Reaction Mechanisms Contribute to the Hydroxylation of Primary Amines by Cytochrome P450?

Use of density functional theory in drug metabolism studies.

Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.

General Transition-State Force Field for Cytochrome P450 Hydroxylation

XMetDB: an open access database for xenobiotic metabolism

Protonation of the proximal histidine ligand in heme peroxidases

Nitrogen inversion barriers affect the N-oxidation of tertiary alkylamines by cytochromes P450.

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2

Mechanism of the N-Hydroxylation of Primary and Secondary Amines by Cytochrome P450

Theoretical Study of the Cytochrome P450 Mediated Metabolism of Phosphorodithioate Pesticides

Branched nanotrees with immobilized acetylcholine esterase for nanobiosensor applications

Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions

Structure-activity relationships and identification of optmized CC-chemokine receptor CCR1, 5, and 8 metal-ion chelators

A comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin

Comment on “binding free energies of inhibitors to iron porphyrin complex as a model for cytochrome p450”

Prediction of Cytochrome P450 Mediated Metabolism of Designer Drugs

Density functional theory study on the formation of reactive benzoquinone imines by hydrogen abstraction.

Enrichment of True Positives from Structural Alerts Through the Use of Novel Atomic Fragment Based Descriptors

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism