{"id":110,"date":"2020-06-14T12:00:38","date_gmt":"2020-06-14T11:00:38","guid":{"rendered":"https:\/\/sciting.eu\/sciting\/?page_id=110"},"modified":"2020-06-14T21:40:54","modified_gmt":"2020-06-14T20:40:54","slug":"machine-learning","status":"publish","type":"page","link":"https:\/\/sciting.eu\/sciting\/samples\/machine-learning\/","title":{"rendered":"Machine Learning"},"content":{"rendered":"\n



THE PROBLEM<\/p>\n\n\n\n

Understanding protein-ligand recognition is crucial in drugs discovery.<\/p>\n\n\n\n

Most of the features used for describing such interactions are parametric.<\/p>\n\n\n\n

This practically means that, if there are not suitable parameters for a particular atom, functional group or interaction, either the calculation fails or a rough approximation is provided. <\/p>\n\n\n\n

We wanted to know whether or not non-parametric chemical descriptors could compete with parametric ones. <\/p>\n\n\n\n



THE SOLUTION<\/p>\n\n\n\n

We tested two different non-parametric descriptors sets by using machine learning algorithms. <\/p>\n\n\n\n

One of such sets provided better results than those obtained with state-of-the-art parametric sets.


<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n



A Python 3 \/ Bash automatic workflow was developed that:<\/p>\n\n\n\n

  1. Downloads and fixes the PDB files.<\/li>
  2. Minimises the protein-ligand binding site.<\/li>
  3. Splits the testing, validation and training sets according to different criteria.<\/li>
  4. Trains machine learning models.<\/li>
  5. Determines which, among thousands of descriptors, contribute more to model accuracy.<\/li>
  6. Plots the results.
    <\/li><\/ol>\n\n\n\n
    \"\"<\/figure>\n\n\n\n
    \"\"<\/figure>\n\n\n\n


    THE OUTCOME<\/p>\n\n\n\n

    The results have been published <\/a>in a peer-reviewed scientific journal.

    <\/p>\n\n\n\n

    \"\"<\/a><\/figure><\/div>\n","protected":false},"excerpt":{"rendered":"

    THE PROBLEM Understanding protein-ligand recognition is crucial in drugs discovery. Most of the features used for describing such interactions are parametric. This practically means that, if there are not suitable parameters for a particular atom, functional group or interaction, either the calculation fails or a rough approximation is provided. We wanted to know whether or […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":79,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-110","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/110","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/comments?post=110"}],"version-history":[{"count":7,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/110\/revisions"}],"predecessor-version":[{"id":152,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/110\/revisions\/152"}],"up":[{"embeddable":true,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/79"}],"wp:attachment":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/media?parent=110"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}