Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-3537

Explore linkage with python library MODELLER

    XMLWordPrintable

    Details

    • Type: Story
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: file format issue
    • Labels:
      None

      Description

      Javier was asking if there are/could be linkage between Jalview and MODELLER (https://salilab.org/modeller/)

      Input to MODELLER is a PIR file with alignment and structure or structure template.

      "MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac."

      B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics 54, John Wiley & Sons, Inc., 5.6.1-5.6.37, 2016.

        Attachments

          Activity

            People

            Assignee:
            jprocter Jim Procter
            Reporter:
            soares Ben Soares
            Votes:
            0 Vote for this issue
            Watchers:
            3 Start watching this issue

              Dates

              Created:
              Updated: