ArticleJournal of computer-aided molecular design2017
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.
Article in Journal of computer-aided molecular design, 2017. 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.
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning.Computational and structural biotechnology journal · 2025Article
- Identification of a Clade-Specific HLA-C*03:02 CTL Epitope GY9 Derived from the HIV-1 p17 Matrix Protein.International journal of molecular sciences · 2024Article
- Elucidating the molecular mechanisms of essential oils' insecticidal action using a novel cheminformatics protocol.Scientific reports · 2023Article
- Scoring Functions for Protein-Ligand Binding Affinity Prediction using Structure-Based Deep Learning: A Review.Frontiers in bioinformatics · 2022Article
- Using diverse potentials and scoring functions for the development of improved machine-learned models for protein-ligand affinity and docking pose prediction.Journal of computer-aided molecular design · 2021Article
- Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle.Biophysical journal · 2020Article
- Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450.International journal of molecular sciences · 2020Article
- graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein-Ligand Complexes.ACS omega · 2020Article
- visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level.BMC bioinformatics · 2020Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions.Journal of computer-aided molecular design · 2019Article
- Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.Journal of computer-aided molecular design · 2018Article
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2 authors.
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Abstract
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and deduce the expansion coefficients from the structural knowledge base using a convex formulation of the optimization problem. Also, for the training set we do not generate false poses with molecular docking packages, but use constant RMSD rigid-body deformations of the ligands inside the binding pockets. This allows the obtained scoring function to be generally applicable to scoring of structural ensembles generated with different docking methods. We assess the Convex-PL scoring function using data from D3R Grand Challenge 2 submissions and the docking test of the CASF 2013 study. We demonstrate that our results outperform the other 20 methods previously assessed in CASF 2013. The method is available at http://team.inria.fr/nano-d/software/Convex-PL/ .
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