DSSP
From Christoph's Personal Wiki
The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment.[1] DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries.
The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure.
Contents
Usage
Note: See Description of the DSSP program for details.
dssp [-na] [-v] pdb_file [dssp_file] dssp [-na] [-v] -- [dssp_file] dssp [-h] [-?] [-V]
Command line options
-na- Disables the calculation of accessible surface.
-c- Classic (pre-July 1995) format.
-v- Verbose.
--- Read from standard input.
-h -?- Prints a help message.
-l- Prints the license information.
-V- Prints version, as in first line of the output.
See also
- InterMap3D — predicts interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein sequences.
- wikipedia:Frenet-Serret formulas (and the curvature and torsion concepts in differential geometry called the kappa-tau framework)
References
- ↑ Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers, 22(12):2577-2637. PMID: 6667333.
Further reading
- Soumpasis DM, Strahm MC (2000). "Efficient identification and analysis of substructures in proteins using the kappa-tau framework: left turns and helix c-cap motifs". J Biomol Struct Dyn, 17(6):965-979. PMID: 10949164.
