Ctrl K

PSSMGen

Generates consistent PSSM and PDB files for protein-protein complexes

6
mentions
2
contributors

Cite this software

DOI:

10.5281/zenodo.3635711

Description

  • Easy-to-use tool to calculate PSSM
  • Generate PSSM files for docking models of protein-protein complexes
  • Generate PSSM-matched PDB files

PSSMGen is geared toward computing the pssm files for all models of a particular protein-protein complex. This tool assumes your files have following structure:
caseID
|_ pdb
|_ fasta
|_ pssm_raw
|_ pssm
|_ pdb_raw
caseID is the ID of protein-protein complex, e.g. PDB ID 1AK4 or CAPRI target ID T161. Only the pdb dir must exist at run time, and it must contain the PDB files of the models generated by HADDOCK. Based on these PDB files, the code will extract protein sequences and generate the FASTA files (stored in the fasta subdir). It will then use the BLAST tool psiblast to compute PSSM (stored in pssm_raw subdir). Finally the sequences from PSSM files and PDB files will be aligned and then the consistent PSSM files and/or PDB files will generated. The consistent PSSM files are stored in pssm subdir. If applicable, the consistent PDB files are stored in pdb subdir, while the original non-consistent PDB files are moved to pdb_raw subdir. You can then use PDB files from pdb and PSSM files from pssm for further analysis.

Keywords
Big data
High performance computing
Optimized data handling
Programming languages
License
</>Source code

Participating organisations

Natural Sciences & Engineering
Natural Sciences & Engineering
Life Sciences
Life Sciences
Netherlands eScience Center

Mentions

Contributors

Contact person

Cunliang Geng
Cunliang Geng

Related projects

DeepRank

Scoring 3D protein-protein interaction models using deep learning

Updated 30 months ago
Finished

Related software

iScore

IS

A framework and predictor based on support vector machine and random walk graph kernel for scoring protein-protein interfaces.

Updated 23 months ago
82 4

pdb2sql

PD

Fast and versatile Python package that leverages SQL queries to parse, manipulate and process biomolecular structure files. The structure files should be in the PDB format and are available on www.rcsb.org.

Updated 39 months ago
8 2