scholarly journals Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling

2020 ◽  
Vol 34 (8) ◽  
pp. 831-839
Author(s):  
Anita Rácz ◽  
György M. Keserű
Keyword(s):  
Machine Learning ◽  
Cytochrome P450 ◽  
Drug Interaction ◽  
Interaction Potential ◽  
Large Scale ◽  
Cytochrome P450 2C9 ◽  
Scale Evaluation ◽  
Consensus Modeling

scholarly journals Assessing Conformer Energies using Electronic Structure and Machine Learning Methods

2020 ◽  
Author(s):  
Dakota Folmsbee ◽  
Geoffrey Hutchison
Keyword(s):  
Machine Learning ◽  
Electronic Structure ◽  
Density Functional ◽  
Large Scale ◽  
Single Point ◽  
Semiempirical Method ◽  
Coupled Cluster ◽  
Scale Evaluation ◽  
Machine Learning Methods ◽  
Electronic Structure Methods

We have performed a large-scale evaluation of current computational methods, including conventional small-molecule force fields, semiempirical, density functional, ab initio electronic structure methods, and current machine learning (ML) techniques to evaluate relative single-point energies. Using up to 10 local minima geometries across ~700 molecules, each optimized by B3LYP-D3BJ with single-point DLPNO-CCSD(T) triple-zeta energies, we consider over 6,500 single points to compare the correlation between different methods for both relative energies and ordered rankings of minima. We find promise from current ML methods and recommend methods at each tier of the accuracy-time tradeoff, particularly the recent GFN2 semiempirical method, the B97-3c density functional approximation, and RI-MP2 for accurate conformer energies. The ANI family of ML methods shows promise, particularly the ANI-1ccx variant trained in part on coupled-cluster energies. Multiple methods suggest continued improvements should be expected in both performance and accuracy.

scholarly journals Assessing Conformer Energies using Electronic Structure and Machine Learning Methods

2020 ◽  
Author(s):  
Dakota Folmsbee ◽  
Geoffrey Hutchison
Keyword(s):  
Machine Learning ◽  
Electronic Structure ◽  
Density Functional ◽  
Large Scale ◽  
Single Point ◽  
Semiempirical Method ◽  
Coupled Cluster ◽  
Scale Evaluation ◽  
Machine Learning Methods ◽  
Electronic Structure Methods

We have performed a large-scale evaluation of current computational methods, including conventional small-molecule force fields, semiempirical, density functional, ab initio electronic structure methods, and current machine learning (ML) techniques to evaluate relative single-point energies. Using up to 10 local minima geometries across ~700 molecules, each optimized by B3LYP-D3BJ with single-point DLPNO-CCSD(T) triple-zeta energies, we consider over 6,500 single points to compare the correlation between different methods for both relative energies and ordered rankings of minima. We find promise from current ML methods and recommend methods at each tier of the accuracy-time tradeoff, particularly the recent GFN2 semiempirical method, the B97-3c density functional approximation, and RI-MP2 for accurate conformer energies. The ANI family of ML methods shows promise, particularly the ANI-1ccx variant trained in part on coupled-cluster energies. Multiple methods suggest continued improvements should be expected in both performance and accuracy.

Herb–drug interaction potential of Berberis aristata through cytochrome P450 inhibition assay

Synergy ◽  
2017 ◽  
Vol 4 ◽  
pp. 1-7 ◽  
Author(s):  
Shiv Bahadur ◽  
Pulok K. Mukherjee ◽  
Subrata Pandit ◽  
S.K. Milan Ahmmed ◽  
Amit Kar
Keyword(s):  
Cytochrome P450 ◽  
Drug Interaction ◽  
Interaction Potential ◽  
Inhibition Assay

Use of Multiple Probes to Assess Transporter- and Cytochrome P450-Mediated Drug–Drug Interaction Potential of the Pangenotypic HCV NS5A Inhibitor Velpatasvir

2015 ◽  
Vol 55 (5) ◽  
pp. 605-613 ◽  
Author(s):  
Erik Mogalian ◽  
Polina German ◽  
Brian P. Kearney ◽  
Cheng Yong Yang ◽  
Diana Brainard ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Drug Interaction ◽  
Interaction Potential ◽  
Ns5a Inhibitor ◽  
Drug Drug Interaction

scholarly journals A Novel PBPK Modeling Approach to Assess Cytochrome P450 Mediated Drug-Drug Interaction Potential of the Cytotoxic Prodrug Evofosfamide

2018 ◽  
Vol 7 (12) ◽  
pp. 829-837 ◽  
Author(s):  
Christian Lüpfert ◽  
Martin Dyroff ◽  
Oliver von Richter ◽  
Dieter Gallemann ◽  
Samer El Bawab ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Drug Interaction ◽  
Interaction Potential ◽  
Pbpk Modeling ◽  
Modeling Approach ◽  
Drug Drug Interaction
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