xialab-ahu / spdh

            SPDH                

SPDH ├─conf #configuration file ├─datasets #All data │ ├─train_sequence #The sequence files used for the training set │ └─test_sequence #The sequence files used for the test set ├─feature #AAindex feature ├─model #model data file ├─outwhd #output file └─src #code folder

[Publication Title] Predicting hot spot residues at protein-DNA binding interfaces based on sequence information

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[Environment] This software needs to run on Linux A python2.7 environment is required

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[Data] Data comes from PrPDH. (http://bioinfo.ahu.edu.cn:8080/PrPDH/downloads/PrPDH_v1_benchmark.zip)

train_pos_label.csv	is the preprocessed training set data and labels  
test_pos_label.csv	is the preprocessed test set data and labels 
train_feature.csv	is the feature of the training set data
test_feature.csv	is the feature of the test set data
train_sequence/ 	is the sequence file used in the training set
test_sequence/		is the sequence file used in the test set

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[REQUIREMENTS] Need to download and install the following software

SPIDER2 https://servers.sparks-lab.org/downloads/SPIDER2_local.tgz

Blast-2.2.18 https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.18/blast-2.2.18-x64-linux.tar.gz

ncbi-blast-2.7.1+ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz

Netsurfp-1.0 http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netsurfp And download the library files it needs http://www.cbs.dtu.dk/services/NetSurfP-1.0/data.tar.gz And the blast library files it uses http://www.cbs.dtu.dk/services/NetSurfP-1.0/nr70_db.tar.gz

DISOPRED 3.1 http://bioinfadmin.cs.ucl.ac.uk/downloads/DISOPRED/DISOPRED3.16.tar.gz

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Characteristics of the tool: Spider2_path run_local_blast HSE_run1 Netsurfp_path DISOPRED_path

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conf/ is a configuration file you need change your path, like spider2... feature/ is part of feature, don't move.

model/ is model data file. And Don't move it.

src/ is the code folder, you can change it if you want.

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[example] run----->

python main.py -i 1AAY_A.seq -s3 1aay.i1 -o outScore

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The '-i' is that input you seq. The '-s3' is spider3 output for the input to your sequence file. The '-o' is the output file.