SCpre-seq, an end-to-end sequence-based tool using a residue level mutation-based 3D structure information to assess single point mutation effects on protein thermodynamic stability and applying to dingle-domain monomeric proteins. More information can be checked at the tutorial.
Download Anaconda and install. If your computer has alread installed, pass this step.
Using conda install hhsuite. It is also can be installed by other methods shown on official website, If you have installed, pass this step.
conda install -c conda-forge -c bioconda hhsuite
Install HHsuite database.
mkdir HHsuitDB
cd HHsuitDB
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
mkdir -p UniRef30_2020_06
tar xfz UniRef30_2020_06_hhsuite.tar.gz -C ./UniRef30_2020_06
rm UniRef30_2020_06_hhsuite.tar.gz
Using conda install DSSP programe. (https://anaconda.org/salilab/dssp)
conda install -c salilab dssp
Then to find the execute programe mkdssp. You can change the mkdssp
to dssp using cp command by yourself.
whereis mkdssp
We also recommend to install BLAST++ using conda. To install this package with conda run one of the following:
conda install -c bioconda blast
conda install -c bioconda/label/cf201901 blast
Install BLAST++ database.
mkdir PsiblastDB/
cd PsiblastDB
wget https://ftp.ncbi.nlm.nih.gov/blast/db/swissprot.tar.gz
wget https://ftp.ncbi.nlm.nih.gov/blast/db/swissprot.tar.gz.md5
tar -zxvf swissprot.tar.gz
rm swissprot.tar.gz
rm swissprot.tar.gz.md5
git clone https://github.com/hurraygong/MU3DSP.git
cd SCpre-seq
python StatGetPDBlist.py -p residueposition -w wildtyperesidue -m mutationresidue -o outfilename -s sequencepath --pdbpath pdbfilepath --dssppath dsspfilepath --dsspbin mkdssp-path --psiblastbin psiblast-path --hhblitsbin hhblits-path --psiblastout psioutfile-path --psiblastpssm pssmoutfile-path --psiblastdb swissprot-path --hhblitsdb UniRef30_2020_06-path --hhblitsout hhblitoutpath --hhblitshhm hhmoutfilepath