Efflux ATP Binding

Usage

Preprocessing

Generate PSSM using Blast

1. Make sure you've already the fasta files from Uniprot
2. Make sure you've already set blast tool and NR DB
3. run this command to generate pssm from fasta using blast

python pssmbyblast.py <fastadir>

Generate position list of binding site

python generateposlist.py

Filter pssm based on the similarity result

1. Make sure you've already run blastclust tool to generate similarity result
2. run this script to filter the pssm files

python filterpssm.py <resultsimilarityfile>

Generate Libsvm from pssm files

1. run this script to generate libsvm files from pssm

python pssm_to_libsvm.py <folderofpssm> <windowssize>

Generate csv from libsvm

1. run this script to generate csv as our final dataset

python libsvm_to_csv.py <folderoflibsvm>

Generate Dataset

1. run this script to generate dataset as training, validation and independent with customize ratio

python generatedataset.py <folderofcsv> <ratio>

Run some algorithm

We provide some algorithm to try such as CNN, ResNet, VGG and DenseNet.

See this current result.

Algo	ACC	TN	FN	TP	FP	Specitivity	Sensitivity	MCC	AUC
CNN	100 %	4177	1	48	1	100 %	98 %	0.979
ResNet 18	99 %	4176	1	48	2	100 %	98 %	0.969
ResNet 50	99 %	4176	1	48	2	100 %	98 %	0.969
VGG 16
VGG 19
DenseNet