https://m1p.org/index.php?action=history&feed=atom&title=Projects%2FCASF%3A_Comparative_assessment_of_scoring_functions 2026-04-13T08:51:05Z Revision history for this page on the wiki MediaWiki 1.34.0 https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=1457&oldid=prev 2024-02-16T21:14:25Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en-GB"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 21:14, 16 February 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>=Problem 53=</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">{{#seo:</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> |title=Comparative assessment of scoring functions</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> |titlemode=replace</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> |keywords=Comparative assessment of scoring functions</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> |description=Projects/CASF: Comparative assessment of scoring functions for protein-ligand docking problem </ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> }}</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">=</ins>=Problem 53<ins class="diffchange diffchange-inline">=</ins>=</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Title: CASF: Comparative assessment of scoring functions for protein-ligand docking problem  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Title: CASF: Comparative assessment of scoring functions for protein-ligand docking problem  </div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Problem: We have to create a scoring model^ which predicts will the couple protein and ligand be <del class="diffchange diffchange-inline">a </del>complex.   </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Problem: We have to create a scoring model^ which predicts will the couple protein and ligand be complex.   </div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Data: The project code <del class="diffchange diffchange-inline">contain </del>two parts. The first one is [https://github.com/Intelligent-Systems-Phystech/ProbabilisticMetricSpaces ProbalilisticMetricSpaces], the second <del class="diffchange diffchange-inline">on </del>in a notebook, by request.  </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Data: The project code <ins class="diffchange diffchange-inline">contains </ins>two parts. The first one is [https://github.com/Intelligent-Systems-Phystech/ProbabilisticMetricSpaces ProbalilisticMetricSpaces], <ins class="diffchange diffchange-inline">and </ins>the second <ins class="diffchange diffchange-inline">one is </ins>in a notebook, by request.  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* References:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* References:</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l9" >Line 9:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* 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].</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* 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].</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Method: We propose a novel approach to reconstruct <ins class="diffchange diffchange-inline">the </ins>distribution of bonding angles and solve the scoring problem as a problem of metric classification.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Current goals=</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Current goals=</div></td></tr> </table>

Vs https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=480&oldid=prev 2021-02-19T09:06:15Z

<p><span dir="auto"><span class="autocomment">Seminars</span></span></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en-GB"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 09:06, 19 February 2021</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l16" >Line 16:</td> <td colspan="2" class="diff-lineno">Line 16:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># To develop the model and beat the tests</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># To develop the model and beat the tests</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Seminars=</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Seminars=</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># [http://www.machinelearning.ru/wiki/images/e/ed/Strijov2020CASFIntro.pdf Introduction to the CASF competition project, 20.08.2020]</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># [http://www.machinelearning.ru/wiki/images/e/ed/Strijov2020CASFIntro.pdf Introduction to the CASF competition project, 20.08.2020<ins class="diffchange diffchange-inline">], [https://www.youtube.com/watch?v=pyanoXgKB_g video, Ru</ins>]</div></td></tr> </table>

Wiki https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=360&oldid=prev 2020-08-20T16:27:49Z

<p><span dir="auto"><span class="autocomment">Current goals</span></span></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en-GB"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:27, 20 August 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l15" >Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># To combine the probability distributions with the basic code</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># To combine the probability distributions with the basic code</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># To develop the model and beat the tests</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># To develop the model and beat the tests</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">=Seminars=</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"># [http://www.machinelearning.ru/wiki/images/e/ed/Strijov2020CASFIntro.pdf Introduction to the CASF competition project, 20.08.2020]</ins></div></td></tr> </table>

Wiki https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=356&oldid=prev 2020-08-18T16:29:34Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en-GB"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:29, 18 August 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8" >Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# 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]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Basic solution: The solution is a linear combination, it is described in [https://hal.inria.fr/hal-01591154/ this paper].</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Basic solution: The solution is a linear combination, it is described in [https://hal.inria.fr/hal-01591154/ this paper<ins class="diffchange diffchange-inline">], and [https://www.overleaf.com/project/5bdc5b1a7caa0c4c233790ed draft</ins>].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov</div></td></tr> </table>

Wiki https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=353&oldid=prev 2020-08-18T16:25:36Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en-GB"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:25, 18 August 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Problem 53=</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Problem 53=</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Title:<del class="diffchange diffchange-inline"> Comparison analysis </del>scoring functions for docking problem  </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Title:<ins class="diffchange diffchange-inline"> CASF: Comparative assessment of </ins>scoring functions for <ins class="diffchange diffchange-inline">protein-ligand </ins>docking problem  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Problem: We have to create a scoring model^ which predicts will the couple protein and ligand be a complex.   </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Problem: We have to create a scoring model^ which predicts will the couple protein and ligand be a complex.   </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* 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.  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* 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.  </div></td></tr> </table>

Wiki https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=351&oldid=prev 2020-08-18T16:23:20Z

<p>Wiki moved page <a href="/index.php/Projects/CASF:_Comparison_analysis_scoring_functions" class="mw-redirect" title="Projects/CASF: Comparison analysis scoring functions">Projects/CASF: Comparison analysis scoring functions</a> to <a href="/index.php/Projects/CASF:_Comparative_assessment_of_scoring_functions" title="Projects/CASF: Comparative assessment of scoring functions">Projects/CASF: Comparative assessment of scoring functions</a></p> <table class="diff diff-contentalign-left" data-mw="interface"> <tr class="diff-title" lang="en-GB"> <td colspan="1" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="1" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:23, 18 August 2020</td> </tr><tr><td colspan="2" class="diff-notice" lang="en-GB"><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

Wiki https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=350&oldid=prev 2020-08-18T16:21:59Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en-GB"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:21, 18 August 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l11" >Line 11:</td> <td colspan="2" class="diff-lineno">Line 11:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">=Current goals=</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"># To run the basic code with slight model variations and repeat the computational experiment</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"># To combine the probability distributions with the basic code</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"># To develop the model and beat the tests</ins></div></td></tr> </table>

Wiki https://m1p.org/index.php?title=Projects/CASF:_Comparative_assessment_of_scoring_functions&diff=349&oldid=prev 2020-08-18T16:19:25Z

<p>Created page with &quot;=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 lig...&quot;</p> <p><b>New page</b></p><div>=Problem 53=<br /> * Title: Comparison analysis scoring functions for docking problem <br /> * Problem: We have to create a scoring model^ which predicts will the couple protein and ligand be a complex. <br /> * 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. <br /> * References:<br /> *# 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]<br /> *# 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[https://pubs.acs.org/doi/10.1021/acs.jcim.5b00339]<br /> *# 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]<br /> *# 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]<br /> * Basic solution: The solution is a linear combination, it is described in [https://hal.inria.fr/hal-01591154/ this paper].<br /> * Method: We propose a novel approach to reconstruct distribution of bonding angles and solve the scoring problem as a problem of metric classification.<br /> * Authors: Sergei Grudinin, Maria Kadukova, and Vadim Strijov</div>

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