Problem 53

Title: Comparison analysis scoring functions for docking problem
Problem: We have to create a scoring model^ which predicts will the couple protein and ligand be a complex.
Data: The project code contain two parts. The first one is ProbalilisticMetricSpaces, the second on in a notebook, by request.
References:
1. Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization by Maria Kadukova and Sergei Grudinin, 2017[1]
2. Predicting Binding Poses and Affinities in the CSAR 2013–2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential by Sergei Grudinin et al, 2016[2]
3. Comparative Assessment of Scoring Functions: The CASF-2016 Update by Minyi Su et al., 2018[3]
4. Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4 Maria Kadukova et al., 2020[4]
Basic solution: The solution is a linear combination, it is described in this paper.
Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.
Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov

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