Difference between revisions of "Projects/CASF: Comparative assessment of scoring functions"

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=Problem 53=
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|description=Projects/CASF: Comparative assessment of scoring functions for protein-ligand docking problem
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==Problem 53==
 
* Title: CASF: Comparative assessment of scoring functions for protein-ligand docking problem  
 
* 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.   
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* Problem: We have to create a scoring model^ which predicts will the couple protein and ligand be complex.   
* Data: The project code contain two parts. The first one is [https://github.com/Intelligent-Systems-Phystech/ProbabilisticMetricSpaces ProbalilisticMetricSpaces], the second on in a notebook, by request.  
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* Data: The project code contains two parts. The first one is [https://github.com/Intelligent-Systems-Phystech/ProbabilisticMetricSpaces ProbalilisticMetricSpaces], and the second one is in a notebook, by request.  
 
* References:
 
* References:
 
*# 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[https://link.springer.com/article/10.1007/s10822-017-0068-8]
 
*# 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[https://link.springer.com/article/10.1007/s10822-017-0068-8]
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*# Comparative Assessment of Scoring Functions: The CASF-2016 Update by  Minyi Su et al., 2018[https://pubs.acs.org/doi/10.1021/acs.jcim.8b00545]
 
*# Comparative Assessment of Scoring Functions: The CASF-2016 Update by  Minyi Su et al., 2018[https://pubs.acs.org/doi/10.1021/acs.jcim.8b00545]
 
*# Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4 Maria Kadukova et al., 2020[https://hal.archives-ouvertes.fr/hal-02434514]
 
*# Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4 Maria Kadukova et al., 2020[https://hal.archives-ouvertes.fr/hal-02434514]
* Basic solution: The solution is a linear combination, it is described in [https://hal.inria.fr/hal-01591154/ this paper].
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* Basic solution: The solution is a linear combination, it is described in [https://hal.inria.fr/hal-01591154/ this paper], and [https://www.overleaf.com/project/5bdc5b1a7caa0c4c233790ed draft].
* Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.
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* Method: We propose a novel approach to reconstruct the distribution of bonding angles and solve the scoring problem as a problem of metric classification.
 
* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov
 
* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov
 
=Current goals=
 
=Current goals=
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# To combine the probability distributions with the basic code
 
# To combine the probability distributions with the basic code
 
# To develop the model and beat the tests
 
# To develop the model and beat the tests
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=Seminars=
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# [http://www.machinelearning.ru/wiki/images/e/ed/Strijov2020CASFIntro.pdf Introduction to the CASF competition project, 20.08.2020], [https://www.youtube.com/watch?v=pyanoXgKB_g video, Ru]

Latest revision as of 00:14, 17 February 2024

Problem 53

  • 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 complex.
  • Data: The project code contains two parts. The first one is ProbalilisticMetricSpaces, and the second one is 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, and draft.
  • Method: We propose a novel approach to reconstruct the distribution of bonding angles and solve the scoring problem as a problem of metric classification.
  • Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov

Current goals

  1. To run the basic code with slight model variations and repeat the computational experiment
  2. To combine the probability distributions with the basic code
  3. To develop the model and beat the tests

Seminars

  1. Introduction to the CASF competition project, 20.08.2020, video, Ru