Journal article Open Access

Machine Learnable Fold Space Representation based on Residue Cluster Classes

Corral-Corral, Ricardo; Del Rio, Gabriel; Chavez, Edgar


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/1175d5c6-5b40-4c8a-8a92-8829f6e3cbc3/MachineLearnableFoldSpaceRepresentationbasedonRCC_.pdf"
      }, 
      "checksum": "md5:00205c1cdf9195587b001eead40573ed", 
      "bucket": "1175d5c6-5b40-4c8a-8a92-8829f6e3cbc3", 
      "key": "MachineLearnableFoldSpaceRepresentationbasedonRCC_.pdf", 
      "type": "pdf", 
      "size": 1362765
    }
  ], 
  "owners": [
    21595
  ], 
  "doi": "10.1016/j.compbiolchem.2015.07.010", 
  "stats": {
    "version_unique_downloads": 181.0, 
    "unique_views": 315.0, 
    "views": 318.0, 
    "version_views": 318.0, 
    "unique_downloads": 181.0, 
    "version_unique_views": 315.0, 
    "volume": 250748760.0, 
    "version_downloads": 184.0, 
    "downloads": 184.0, 
    "version_volume": 250748760.0
  }, 
  "links": {
    "doi": "https://doi.org/10.1016/j.compbiolchem.2015.07.010", 
    "latest_html": "https://zenodo.org/record/50192", 
    "bucket": "https://zenodo.org/api/files/1175d5c6-5b40-4c8a-8a92-8829f6e3cbc3", 
    "badge": "https://zenodo.org/badge/doi/10.1016/j.compbiolchem.2015.07.010.svg", 
    "html": "https://zenodo.org/record/50192", 
    "latest": "https://zenodo.org/api/records/50192"
  }, 
  "created": "2016-05-18T16:19:15+00:00", 
  "updated": "2020-01-20T15:10:31.092992+00:00", 
  "conceptrecid": "632904", 
  "revision": 10, 
  "id": 50192, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.1016/j.compbiolchem.2015.07.010", 
    "description": "<p><strong>Abstract</strong></p>\n\n<p><strong>Motivation</strong></p>\n\n<p>Protein fold space is a conceptual framework where all possible protein folds exist and ideas about protein structure, function and evolution may be analyzed. Classification of protein folds in this space is commonly achieved by using similarity indexes and/or machine learning approaches, each with different limitations.</p>\n\n<p><strong>Results</strong></p>\n\n<p>We propose a method for constructing a compact vector space model of protein fold space by representing each protein structure by its residues local contacts. We developed an efficient method to statistically test for the separability of points in a space and showed that our protein fold space representation is learnable by any machine-learning algorithm.</p>\n\n<p><strong>Availability</strong></p>\n\n<p>An API is freely available at&nbsp;https://code.google.com/p/pyrcc/.</p>", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "title": "Machine Learnable Fold Space Representation based on Residue Cluster Classes", 
    "journal": {
      "volume": "59", 
      "year": "2015", 
      "pages": "1-7", 
      "title": "Computational Biology and Chemistry"
    }, 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "632904"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "50192"
          }
        }
      ]
    }, 
    "keywords": [
      "Computational Biology", 
      "Machine Learning", 
      "Protein Structure", 
      "CATH", 
      "SCOP", 
      "Protein Fold Space", 
      "Sperner Family"
    ], 
    "publication_date": "2015-12-01", 
    "creators": [
      {
        "affiliation": "Department of Biochemistry and Structural Biology, Instituto de Fisiologa Celular, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico D. F., M\u00e9xico", 
        "name": "Corral-Corral, Ricardo"
      }, 
      {
        "affiliation": "Department of Biochemistry and Structural Biology, Instituto de Fisiologa Celular, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico D. F., M\u00e9xico", 
        "name": "Del Rio, Gabriel"
      }, 
      {
        "affiliation": "Centro de Investigaci\u00f3n Cient\u00edfica y de Educaci\u00f3n Superior de Ensenada, M\u00e9xico", 
        "name": "Chavez, Edgar"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "subtype": "article", 
      "type": "publication", 
      "title": "Journal article"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.5281/zendoo.50193", 
        "relation": "isSupplementedBy"
      }
    ]
  }
}
318
184
views
downloads
Views 318
Downloads 184
Data volume 250.7 MB
Unique views 315
Unique downloads 181

Share

Cite as