Projects/CASF: Comparative assessment of scoring functions
From My first scientific paper
- Title: CASF: Comparative assessment of scoring functions for protein-ligand 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.
- 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
- 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
- Comparative Assessment of Scoring Functions: The CASF-2016 Update by Minyi Su et al., 2018
- Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4 Maria Kadukova et al., 2020
- Basic solution: The solution is a linear combination, it is described in this paper, and draft.
- 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
- To run the basic code with slight model variations and repeat the computational experiment
- To combine the probability distributions with the basic code
- To develop the model and beat the tests