conservation_python

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Jon Wright, IBMS, Academia Sinica, Taipei, 11529, Taiwan

These files are licensed under the GLP ver 3, essentially you have the right

to copy, modify and distribute this script but all modifications must be offered

back to the original authors

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This is an implimentation of the consurf system This code has been tested on Centos 7.x and Ubuntu 22.04 as a standalone desktop and on a multi-core system under PBS

Requirements: python3 with BioPython (such as anaconda), uniref90 db, HMMER, CD-Hit, Mapsci, Protest and rate4site

It takes a single chain pdb file (often provided from critires) or a single chain fasta file It uses the 300 top acceptable homologs

Each CS run must be done in a separate directory with a fasta or pdb file as the input

To run it if you have a pdb coordinate file as: $consurf_scripts/consurf_home.sh file.pdb

To run it if you have a fasta file as: $consurf_scripts/consurf_home.sh file.fasta

If you want to use the SEQRES records from the pdb file instead of the ATOM records then use: $consurf_scripts/consurf_seqres.sh file.pdb

Note the numbering will run from 1->X however

Options used by programs are:

jackhmmer: -E 0.0001 --domE 0.0001 --incE 0.0001 -N 1

cdhit: -c 0.95

mafft-linsi: --quiet --localpair --maxiterate 1000 --namelength 30

protest: -JTT -LG -MtREV -Dayhoff -WAG -CpREV -S 1

rate4site: -ib -zn $MODEL_FROM_PROTEST -bn