This 3D proximity tool can be used to identify mutation hotspots from the linear protein sequence and correlates the hotspots with known or potentially interacting domains and mutations. Mutation-mutation and mutation-drug clusters can also be identified and viewed.
Program: HotSpot3D - 3D mutation proximity analysis program.
Version: V0.4
Author: Beifang Niu, John Wallis, Adam D Scott, & Sohini Sengupta
Usage: hotspot3d <command> [options]
Key commands:
search -- 3D mutation proximity searching
post -- Post-processing on pairwise data
cluster -- Determine clusters from HotSpot3D inter, intra, and druggable pairwise data
sigclus -- Determine significance of clusters
summary -- Determine cluster-level measures
visual -- Visulization of 3D proximity
drugport -- Parse drugport database
uppro -- Update proximity files
calpro -- Calculate proximity file for one UniProt ID
calroi -- Generate region of interest (ROI) information
statis -- Calculate p_values for pairs of mutations
anno -- Add region of interest (ROI) annotation
trans -- Add transcript annotation
homo -- Add homology PDB structures
cosmic -- Add COSMIC annotation to proximity file
prior -- Prioritization
help -- this message
SUPPORT For user support please mail [email protected]
Prerequisites:
In order to install HotSpot3D package, first install CPANM (cpanm - get, unpack build and install modules from CPANM) NOTE: Some steps may require adding --force to install successfully.
sudo apt-get install cpanminus
Another way to install cpanminus is to just download it, as per the installer
curl -LO http://xrl.us/cpanm
chmod +x cpanm
Or by using cpan
cpan App::cpanminus
Intall Perl5 local lib
cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
Intall LWP::Simple module
sudo apt-get install libwww-perl
Intall Test::Most module
wget http://search.cpan.org/CPAN/authors/id/O/OV/OVID/Test-Most-0.34.tar.gz
cpanm Test-Most-0.34.tar.gz
Install HotSpot3D package:
git clone https://github.com/ding-lab/hotspot3d
cd hotspot3d
cpanm HotSpot3D-#.#.tar.gz
(Installations under some organizations may use an internal perl version. To make use of the /usr/ perl, edit the first line of ~/perl5/bin/hotspot3d. from: #!/org/bin/perl to: #!/usr/bin/perl)
Preprocessing procedure
-
Run drugport module to parse Drugport data and generate a drugport parsing results flat file :
hotspot3d drugport --pdb-file-dir=pdb_files_dir --output-file=drugport_parsing_results_file
-
Run 3D proximity calculation ( this step needs one output directory to store all of the data from the pre-processing procedure and one directory which contains pdb files downloaded from the PDB website. This step will automatically download PDB files if the necessary PDB file is not yet in the pdb files directory) :
hotspot3d uppro --output-dir=preprocessing_output --pdb-file-dir=pdb_files_dir --drugport-file=drugport_parsing_results_file --max-3d-dis=100 1>hotspot3d.preprocessing.t.err 2>hotspot3d.preprocessing.t.out
-
Calculate protein domain information for each UniProt ID :
hotspot3d calroi --output-dir=preprocessing_output
-
Significance determination calculation :
hotspot3d statis --output-dir=preprocessing_output
-
Add protein domain annotation information to 3D proximity information :
hotspot3d anno --output-dir=preprocessing_output
-
Choose transcripts based on the alignment between Uniprot sequence and human peptides sequences :
hotspot3d trans --output-dir=preprocessing_output
-
Add cosmic v67 information to 3D proximity results :
mkdir preprocessing_output/cosmic cp COSMIc/cosmic_67_for_HotSpot3D_missense_only.tsv.bz2 ./preprocessing_output/cosmic/ cd ./preprocessing_output/cosmic/ bzip2 -d cosmic_67_for_HotSpot3D_missense_only.tsv.bz2 hotspot3d cosmic --output-dir=preprocessing_output
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Prioritization :
hotspot3d prior --output-dir=preprocessing_output --p-value=0.1 --3d-dis=20 --linear-dis=0.5
3D proximity searching based on prioritization results and visualization
-
Proximity searching (acquire proximity information for input mutations):
hotspot3d search --maf-file=pancan19_input.maf --data-dir=preprocessing_output --output-prefix=pancan19 --skip-silent 1>pancan19.t.out 2>pancan19.t.err
-
Post-processing of pairwise data (required for cluster step):
hotspot3d post --maf-file=pancan19_input.maf --input-prefix=pancan19
-
Cluster pairwise data:
hotspot3d cluster --inter-intra-proximity-file=interactions_file --data-location-file=location_data --output-file=clustering.out --target-nontarget-file=drug_data_file
-
Cluster significance calculation:
hotspot3d sigclus --prep-dir=preprocessing_output --pairwise=pairwise_file --clusters=clusters_file --output=output_file
-
Clustering Summary:
hotspot3d summary --clusters-file=cluster_file --output-file=output_summary
-
Visualization:
hotspot3d visual --pymol-dir=/usr/bin/pymol --output-dir=pymol_out --pdb-dir=pdb_files_dir