BioInformatics File Format

sam

• sam/bam/cram :
• BCFtools: BCF2/VCF/gVCF
• VCF: Variant call format. Mutation centric view

ChemInformatics File Format

PDB

Sample protein:
1tii		A 900+ residues protein, not huge, but a sizable molecule for testing 3D rendering (especially in space filling model)

11AS, 117E	Some pdb file around size of Haemoglobin

1A00            Hemoglobin
1z1g            Topoisomerases, a large protein, "Molecule of the Month" for Dec 2006.

.smi

SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. Some examples are:o
CC  			ethane  	
[OH3+]  		hydronium ion
c1ccccc1  		benzene  	
N[C@H](C)C(=O)O  	D-alanine
COc1cc(cc(OC)c1OC)C(=O)N\N=C(/C)\c2ccc(cc2)S(=O)(=O)N[C@@H](C)C(=O)O	some carboxylic acid
                  

OpenEye Omega take .smi input smiles and produces .oeb.gz files.

.oeb

.oeb receptor file containing active site for docking.
Probably OpenEye propietary.  Fred can open these files (and maybe ROCS?)

BioInformatics

[Doc URL: http://psg.ask-margo.com/sci-file.html]
(cc) Tin Ho. See main page for copyright info.

---