INSTALLATION AND IMPLEMENTATION OF DAMpred (Copyright 2018 by Zhang Lab, University of Michigan, All rights reserved) 1. How to install the DAMpred? 1) Install DAMpred suite a) download the DAMpred package 'DAMpred.tar.bz2' from http://zhanglab.dcmb.med.umich.edu/DAMpred/download and unpack DAMpred.tar.bz2 by > tar -xvf DAMpred.tar.bz2 the root path of this package is called $dampred, e.g. /home/liquan/DAMpred. You should have all the programs under this directory. You can install the package at any location on your computer. b) to modify $dampred/bin/runDAMpred.pl file and set some paths, eg: $usrname = "liquan" #your user name which is useful when making tmp dir. c) export PYTHONPATH=$PYTHONPATH:$dampred/bin/python e.g. $dampred = "/home/liquan/DAMpred" $bindir = "$dampred/bin" 2) Download DAMpred library We recommend putting the library files under the path /home/yourname/lib. the root of these libraries is called $libdir, e.g. /home/liquan/DAMpred/lib a) > cd $libdir > wget http://zhanglab.dcmb.med.umich.edu/DAMpred/lib/human.tar.bz2 > tar -xvf human.tar.bz2 > wget http://zhanglab.dcmb.med.umich.edu/DAMpred/lib/pdb.tar.bz2 > tar -xvf pdb.tar.bz2 Note: What follows are the steps for installing other package. After that you should modify $bindir/python/userConfig.py based on the locations of packages. 3) Install I-TASSER Suite a) Download I-TASSER Suite 'I-TASSER5.1.tar.bz2' from http://zhanglab.dcmb.med.umich.edu/I-TASSER/download, and unpack 'I-TASSER5.1.tar.bz2' in $dampred by > cd $bindir > tar -jxvf I-TASSER5.1.tar.bz2 The root path of this package is called $i_tasser, e.g. /home/liquan/DAMpred/bin/I-TASSER5.1. b) Download I-TASSER library files from a perl script 'download_lib.pl' provided in the I-TASSER package for automated library download and update of the libraries. We recommend putting the library files under the path /home/yourname/lib by > cd $bindir > $i_tasser/download_lib.pl -libdir $dampred/lib -P true -B false -N true the root of these libraries is called $libdir, e.g. /home/liquan/DAMpred/lib 4）Install haad >cd $bindir >wget http://zhanglab.dcmb.med.umich.edu/HAAD/haad 5) Install JSD_concavity > cd $bindir/JSD_concavity > wget http://compbio.cs.princeton.edu/concavity/concavity_distr.tar.gz > tar -xzvf concavity_distr.tar.gz > cd concavity_distr > make clean > make > cp concavity_distr/bin/x86_64/concavity $bindir/JSD_concavity/ 6) Install sefMutation > cd $bindir/sefMutation > wget http://zhanglab.dcmb.med.umich.edu/DAMpred/lib/data.tar.bz2 > tar -xvf data.tar.bz2 Please set the correct PATH $bindir/sefMutation/ in dirLinux.txt 7) Third-party software installation: While the majority of programs in the package 'DAMpred.tar.bz2' are developed in the Zhang Lab here in the permission of use is released, there are some programs and databases which were developed by third-party groups. You may experience installation problems, please check the third-party websites. a) Install 2.2.31 blast i) blast tools >cd $bindir >wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz >tar xzvf ncbi-blast-2.2.31+-x64-linux.tar.gz >rm ncbi-blast-2.2.31+-x64-linux.tar.gz ii) download uniref90.fasta and makeblastdb b）Install Pfam > cd $bindir > wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz > tar -zxvf PfamScan.tar.gz > rm PfamScan.tar.gz > cd $bindir/PfamScan Based on the README of PfamScan to sucefully install pfamscan including pfam and pfamHMM dataset c) Install Psic i)get cluster tools which will be used by Psic > cd $bindir > wget http://www.clustal.org/omega/clustalo-1.2.0-Ubuntu-x86_64 ii) install psic > cd $bindir > wget https://rostlab.org/debian/pool/non-free/p/psic/psic_1.0-rg1.tar.gz > tar -xzf psic_1.0-rg1.tar.gz > cd psic-1.0/ > make > make install d) Installing SCWRL4.0 Just fill out the form and click "I agree" from http://dunbrack.fccc.edu/scwrl4/license/index.html, you will be sent in e-mail a download link only after your liense application is reviewed by SCWRL4 team. If you get the download Page, click the link "Linux Command-line Installer [23 MB]: supports 32bit and 64 bit", put it in the $bindir path. > cd $bindir > chmod a+x install_Scwrl4_Linux > ./install_Scwrl4_Linux Welcome to Scwrl4 installation wizard! Please specify the full path location where Scwrl4 files should be written to. Before you continue the installation, please make sure you have writing privileges for the destination path. Warning: If the specified path contains the previous Scwrl4 intallation, the previously installed files will be overwritten. Press press 'Enter' to interrupt the installation or provide the installation path. The full path is prefered (e.g., /usr/local/bin/scwrl4 or /home/user/scwrl4): $dampred/scwrl4 Scwrl4 files will be written to /home/liquan/DAMpred/bin/scwrl4 Is this correct? [ Y/N ]Y Please specify the license holder of this Scwrl4 copy: (ENTER) ...... >rm install_Scwrl4_Linux e) Installing scikit-learn i) Scikit-learn requires: Python (>= 2.6 or >= 3.3), NumPy (>= 1.6.1), SciPy (>= 0.9) (http://scikit-learn.org/stable/install.html); In the download webpage https://pypi.python.org/pypi/scikit-learn/0.19, you can downlod scikit-learn-0.19.tar.gz by the link: scikit-learn-0.19.tar.gz or > wget https://files.pythonhosted.org/packages/c2/38/e3b0333e661ab411545583cb24940223917fe7ffc9c68a77730dce3b10b0/scikit-learn-0.19.0.tar.gz ii) > tar zxvf scikit-learn-0.19.tar.gz > cd scikit-learn-0.19 > python setup.py install > rm scikit-learn-0.19.tar.gz 2. How to run the DAMpred? 1) make a file, where protein fasta (.fasta) shuld be stored. eg: $dampred/example 2) Main script for runing DAMpred is $bindir/runDAMpred.pl. Run it dirctly without arguments will output the help information. 3) The following arguments must be set. One example is: "$bindir/runDAMpred.pl -inputdir $dampred/example -seq example.fasta -mutation mutation.txt" 4) The sesult will be shown as below ##################################################################################################### # DAMpred Result # # # # protein position wild-type mutant-type Sd Sn Sdiff prediction # # example 3 M K 0.432 0.731 -0.113 neutral # # example 16 V E 0.867 0.180 0.548 disease # # # # the result is saved in final.result # # # ##################################################################################################### DAMpred USAGE: ===================== Mandatory arguments: ===================== ./runDAMpred.pl -inputdir datadir -seq seqname.fasta -mutation mutation -datadir: this is the directory where your input sequence \"proteinname.fasta\" and inoput mutation \"mutation.txt\" are located, and the final results should be saved -seq: the name of protein sequence in raw format and one letter code (the protein sequence code must be saved in datadir) -mutation: the name of mutationfile filled by the single-point muation information including: the wild-type residue, the position number of the residue that undergoes mutation and the mutant residue, eg, A44T ================== Optional arguments: ================== -runstyle default value is \"serial\" which means running I-TASSER simulation sequentially, \"parallel\" means running I-TASSER simulations in parallel, distributed on cluster nodes We suggest testing your installation first with a short sequence (e.g., about 40 residues) before running production jobs for your proteins. An example command for running I-TASSER using a seq \"example.fasta\" under the folder /home/XXX/DAMpred/example $bindir/runDAMpred.pl -inputdir $dampred/example -seq example.fasta -mutation mutation.txt