README

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 and webserver.

Clone the package

git clone https://github.com/hurraygong/MU3DSP.git
cd MU3DSP

Install dependencies

1. Install HHsuite

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

2. Install DSSP

Using conda install DSSP programe (https://anaconda.org/salilab/dssp). It is also can be installed by other methods shown on official website, If you have installed, pass this step.

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

3.Install BLAST++

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

It is also can be installed by other methods shown on official website, If you have installed, pass this step.

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

Usage

If provide MSA files with hhm format from HHblits. It can run with:

  python MU3DSP.py -p residueposition -w wildtyperesidue -m mutationresidue -o -s sequencepath --pdbpath pdbfilepath --dssppath dsspfilepath --dsspbin mkdssp-path --psiblastbin  psiblast-path --hhblitsbin hhblits-path --psiblastout psioutfile-path --psiblastpssm pssmoutfile-path --psiblastdb swissprot-path --hhblitshhm hhmoutfile-path --hhmfile HHblits-hhm-file --printout

For example:

    python MU3DSP.py -p 9 -w Q -m H -s ./examples/SEQ/2ocj_A.fasta --pdbpath ./examples/PDBtest --dssppath ./examples/DSSPtest --dsspbin dssp --psiblastbin  psiblast --hhblitsbin hhmake --psiblastout ./examples/psiout --psiblastpssm ./examples/pssmout --psiblastdb ./PsiblastDB/swissprot --hhblitshhm ./examples/hhmout --outfilepath ./examples/2ocj_Q9H.npy --hhmfile /root/MU3DSP/examples/2ocj_A.hhm --printout

If provide fasta files and HHblits is accessable.

    python MU3DSP.py -p 9 -w Q -m Y --hhsuite True --outfilepath /root/MU3DSP/tmp/2ocj_A_Q9Y.npy -s /root/MU3DSP/tmp/2ocj_A.fasta --G2s --hhmfile /root/MU3DSP/examples/2ocj_A.hhm --pdbpath ./examples/PDBtest --dssppath ./examples/DSSPtest --dsspbin mkdssp --psiblastbin psiblast --psiblastout ./examples/psiout --psiblastpssm ./examples/pssmout --psiblastdb ../blastDB/swissprot --hhblitsdb ../HHblitDB/UniRef30_2020_06 --hhblitsout ./examples/hhblitout --hhblitshhm ./examples/hhmout -o --printout

Because the mutation-based structures are real-time, the DDG will changes with the structures changes and G2s update, we trained MU3DSP-S1676 with S1676 dataset at 12 Sep,2020 and MU3DSP-S5296 on 2 Nov,2022.

References