1. BioShell package
    1. About
    2. Examples gallery
    3. cookbook
    4. API (doxygen)
  2. SURPASS model
    1. About representation
    2. SURPASS force field

BioShell applications

The idea of bioshell is to extends Linux command line by commands for manipulating bioinformatics data. In the current version the following programs are provided:

  • acorr - calculates autocorrelations based on given scalar and vector - type observables
  • hist - prepares 1D and 2D histograms
  • seqc - converts between sequence formats, such as FASTA, PIR, SEQ; also extracts sequences from PDB. Sequences can be sorted and/or filtered by this tool.
  • clust - hierarchical clustering of various data, e.g. protein models (originaly published as ‘HCPM’)
  • strc - structure converter utility, e.g. extracts chains from PDB
  • str_calc - basic calculations on biomolecular structures. Evaluates angles, distances, contact maps, hydrogen bonds etc.
  • trac - converts trajectories computed by CABS / SURPASS protein modeling software
  • blast_analyse - analyses multiple output files from PsiBlast
  • seq_align - calculates alignments between sequences and sequence profiles