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DNA-PKcs

Integrative threading of protein structure using secondary structure elements PubMed logo PDB-Dev

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tickVerified to work with the latest stable IMP release (2.20.2). The files are also available at GitHub.
Additional software needed to use these files: IMP biopython install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp biopython

UCSF logo To set up the environment on the UCSF Wynton cluster to run this system, run:

module load Sali
module load imp python3/biopython
Tags chemical crosslinks threading

DOI

SSEThread : Integrative threading of protein structure using secondary structure elements

In brief, SSEThread proposes and scores threading solutions to protein structures with ambiguous sequence assignment. It is designed specifically for use on elements of secondary structure (helix, sheet), however any structure that is presumed static is usable.

The method relies upon and is built as a module (IMP.threading) in the Integrative Modeling Platform, of which a custom branch is contained here. It will be eventually incorporated into the main IMP codebase.