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DR-Predictor: Incorporating Flexible Docking with Specialized Electronic Reactivity and Machine Learning Techniques to Predict CYP-Mediated Sites of Metabolism

https://doi.org/10.1021/ci4004688
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Docking to heme proteins
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Reduced vdW Radius Improves Site of Metabolism Predictions Using X‐Ray Structure of CYP2D6
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Substrate binding to cytochromes P450
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Multiple-Ligand Binding in CYP2A6: Probing Mechanisms of Cytochrome P450 Cooperativity by Assessing Substrate Dynamics
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RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4
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RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes
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XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks
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Regioselectivity Prediction of CYP1A2-Mediated Phase I Metabolism
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Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands
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Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6
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Mechanism of Oxidation Reactions Catalyzed by Cytochrome P450 Enzymes
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Empirical Regioselectivity Models for Human Cytochromes P450 3A4, 2D6, and 2C9
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Structure-Based Site of Metabolism Prediction for Cytochrome P450 2D6
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Prediction of Metabolism by Cytochrome P450 2C9: Alignment and Docking Studies of a Validated Database of Substrates
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Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking
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Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences
inferredcites →https://doi.org/10.1021/ml100016xopenalex-snapshot
SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism
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Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6
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Structural basis for ligand promiscuity in cytochrome P450 3A4
inferredcites →https://doi.org/10.1073/pnas.1010693107openalex-snapshot
Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir
inferredcites →https://doi.org/10.1074/jbc.m611692200openalex-snapshot
Adaptations for the Oxidation of Polycyclic Aromatic Hydrocarbons Exhibited by the Structure of Human P450 1A2
inferredcites →https://doi.org/10.1093/bioinformatics/btp140openalex-snapshot
Site of metabolism prediction for six biotransformations mediated by cytochromes P450
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Flexibility analysis of enzyme active sites by crystallographic temperature factors
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Fast Bundle Algorithm for Multiple-Instance Learning
inferredcites →https://doi.org/10.1124/dmd.105.008631openalex-snapshot
COMPARISON OF METHODS FOR THE PREDICTION OF THE METABOLIC SITES FOR CYP3A4-MEDIATED METABOLIC REACTIONS
inferredcites →https://doi.org/10.1126/science.1099736openalex-snapshot
Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone
inferredcites →https://doi.org/10.1145/1390156.1390163openalex-snapshot
Multiple instance ranking
inferredcites →https://doi.org/10.1186/1758-2946-3-1openalex-snapshot
CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures
inferredcites →https://doi.org/10.1186/1758-2946-3-s1-o14openalex-snapshot
De novodesign of molecular wires with optimal properties for solar energy conversion
inferredcites →https://doi.org/10.2174/092986709787002727openalex-snapshot
Structure of Cytochrome P450s and Personalized Drug
inferredcites →https://doi.org/10.2174/138620709788167935openalex-snapshot
Virtual Screening for Cytochromes P450: Successes of Machine Learning Filters

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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