pdb to fasta conversion with Bash

Here is a simple pdb to fasta format conversion tool. The purpose was to extract residue sequence from atomic coordinates (ATOM lines).

Note that the sequence extracted this way corresponds to residues which are really present in the 3D structure. This could be different from the sequence obtained from the …

more ...

Cours docking gros grain [fr]

Cours de "docking gros grain" à destination des étudiants en deuxième année du master Biologie – Informatique à l’Université Paris Diderot – Paris 7.

Le cours est téléchargeable au format PDF [5,8 Mo].

more ...

Ambient occlusion-like with PyMOL

QuteMol allows production of nice realistic molecular pictures. PyMOL could do similar things albeit results are not strictly equivalent. Here is an example taken from the PyMOL wiki that produced the picture above.

fetch 1BTA
set_color oxygen, [1.0,0.4,0.4]
set_color nitrogen, [0.5,0.5,1 …
more ...