Difference between revisions of "DSSP"
(→See also) |
(→The DSSP code) |
||
| Line 4: | Line 4: | ||
==The DSSP code== | ==The DSSP code== | ||
| − | H = alpha helix | + | H = alpha helix |
| − | + | I = 5 helix (pi helix) | |
| − | E = extended strand, participates in beta ladder | + | G = 3-helix (3/10 helix) |
| − | + | ||
| − | + | E = extended strand, participates in beta ladder | |
| − | T = hydrogen bonded turn | + | B = residue in isolated beta-bridge |
| + | |||
| + | T = hydrogen bonded turn | ||
S = bend | S = bend | ||
| + | C = others | ||
A blank in the DSSP secondary structure determination stands for loop or irregular. Loops and irregular elements are often, very incorrectly, called "random coil" or "coil". Many programs, including the PDBFINDER, replace this blank by a C (doing undue justice to the historical artefactual naming of loops and irregular stretches) because one never knows if a blank means loop or no-output, or something-went-wrong. | A blank in the DSSP secondary structure determination stands for loop or irregular. Loops and irregular elements are often, very incorrectly, called "random coil" or "coil". Many programs, including the PDBFINDER, replace this blank by a C (doing undue justice to the historical artefactual naming of loops and irregular stretches) because one never knows if a blank means loop or no-output, or something-went-wrong. | ||
Latest revision as of 17:42, 8 January 2009
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
The DSSP code
H = alpha helix I = 5 helix (pi helix) G = 3-helix (3/10 helix) E = extended strand, participates in beta ladder B = residue in isolated beta-bridge T = hydrogen bonded turn S = bend C = others
A blank in the DSSP secondary structure determination stands for loop or irregular. Loops and irregular elements are often, very incorrectly, called "random coil" or "coil". Many programs, including the PDBFINDER, replace this blank by a C (doing undue justice to the historical artefactual naming of loops and irregular stretches) because one never knows if a blank means loop or no-output, or something-went-wrong.
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.
- Frenet-Serret formulas (and the curvature and torsion concepts in differential geometry called the kappa-tau framework)
- Dynameomics.org
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
- Aharonovsky E, Trifonov EN (2005). "Sequence structure of van der Waals locks in proteins". J Biomol Struct Dyn, 22(5):545-553. PMID: 15702926.
- Day R, Beck DA, Armen RS, Daggett V (2003). "A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary". Protein Sci, 12(10):2150-2160. PMID: 14500873.
- Mathee K, Narasimhan G (2003). "Detection of DNA-binding helix-turn-helix motifs in proteins using the pattern dictionary method". Meth Enzymol, 370:250-264. PMID: 14712650.
- Rigoutsos I, Huynh T, Floratos A, Parida L, Platt D (2002). "Dictionary-driven protein annotation". Nucleic Acids Res, 30(17):3901-3916. PMID: 12202776.
- 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.
