Elementolab/Mutation in 3D structure
1. Download Jmol (binary); unzip and click on jmol.jar
2. Find the 3D structure (.pdb format) and its associated sequence in fasta format
An experimentally-determined structure from PDB is ideal. Alternatively, one can use a predicted structure using homology modeling. You can for example check out ModBase.
3. Load the structure in Jmol
4. Say that your mutated residue is at position 132 in the original amino acid sequence. You need to determine where in the structure it is located. This is not trivial because structures are often determined for truncated proteins only.
We made a script for this purpose. By default, you enter a Refseq ID, it finds the corresponding NP (translated Refseq), aligns it to your fasta sequence (the one used in the structure), then finds the corresponding position.
perl ~/PERL_SCRIPTS/pdb_find_pos_ith_aa_from_seq_in_structure.pl --NM=NM_0148777 \ --pdbfa=PIM1_modbase.fa --pos=132 --protfile=human.proteins.faa
(requires Fasta.pm, Sets.pm, Clustalw.pm etc but also clustalw, blast)
5. Say that the script tells you the counterpart of position 132 in the structure is pos 49. To locate this amino acid in the structure in Jmol, open the console and type
cartoon select 49 wireframe 100 color blue
That's it ... below you can find an example.