ArticleInternational journal of molecular sciences2013
CYP 2D6 binding affinity predictions using multiple ligand and protein conformations.
Article in International journal of molecular sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 30 citations in OpenAlex.
- Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation.Journal of chemical theory and computation · 2020Article
- Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations.Frontiers in molecular biosciences · 2020Article
- A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.Journal of chemical information and modeling · 2019Article
- GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm.International journal of molecular sciences · 2019Article
- Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity.International journal of molecular sciences · 2019Article
- Induced fit for cytochrome P450 3A4 based on molecular dynamics.ADMET & DMPK · 2019Article
- Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.Journal of computer-aided molecular design · 2018Article
- eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.Journal of cheminformatics · 2017Article
- Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors.Journal of chemical information and modeling · 2017Article
- Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions.Journal of molecular modeling · 2016Article
- Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation.PloS one · 2015Article
- The eTOX data-sharing project to advance in silico drug-induced toxicity prediction.International journal of molecular sciences · 2014Article
- Towards automated binding affinity prediction using an iterative linear interaction energy approach.International journal of molecular sciences · 2014Article
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Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs), in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interaction energy (LIE) approach to compute CYP binding affinities from molecular dynamics (MD) simulation. In order to improve sampling of conformational space, we combine results from simulations starting with different relevant protein-ligand geometries. For calculated binding free energies of a set of thiourea compounds binding to the flexible CYP 2D6 isoform, improved correlation with experiment was obtained by combining results of MD runs starting from distinct protein conformations and ligand-binding orientations. This accuracy was obtained from relatively short MD simulations, which makes our approach computationally attractive for automated calculations of ligand-binding affinities to flexible proteins such as CYPs.
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