Pipeline of submission

Prepare

Materials

Create a folder

Create a folder on your computer, this folder would store the result of pipeline analysis.

Create a fasta

Write your sequence to the "SEQUENCE ID.fasta" file in fasta format and move it to "YOUR FOLDER".

Analyze

Physicochemical properties

Open the ProtParam server in your browser (https://web.expasy.org/protparam/), paste your protein sequence into the text box and submit. After the analysis, you can save the result page by pressing ctrl+s in your keyboard. Then rename file to "protparam.html" and move it to "YOUR FOLDER".

Hydrophobicity

Open the ProtScale server in your browser (https://web.expasy.org/protscale/), paste your protein sequence into the text box, choose amino acid scale "Hydropath. / Kyte & Doolittle", leave the other options as default and submit. After the analysis, you can save the result page by pressing ctrl+s in your keyboard and save the ProtScale image. Then rename files to "protscale.html", "protscale.gif" and move them to "YOUR FOLDER".

Subcellular Location

  1. Open the TBpred server in your browser (http://crdd.osdd.net/raghava/tbpred/), paste your protein sequence into the text box, choose the option "Amino Acid Composition Based SVM" and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "tbpred.txt" and move it to "YOUR FOLDER".
  2. Open the SignalP 6.0 server in your browser (https://services.healthtech.dtu.dk/services/SignalP-6.0/), paste your protein sequence into the text box, choose the option "Other", "Long output", "Slow" and submit. After the analysis, you can click "All results compressed (zip)" to download the result. Then rename file to "signalp.zip" and move it to "YOUR FOLDER".
  3. Open the TMHMM 2.0 server in your browser (https://services.healthtech.dtu.dk/services/TMHMM-2.0/). paste your protein sequence into the text box, choose the option "One line per protein" and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "tmhmm.txt" and move it to "YOUR FOLDER".
  4. Open the SecretomeP 2.0 server in your browser (https://services.healthtech.dtu.dk/services/SecretomeP-2.0/), paste your protein sequence into the text box, leave the options as default and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "secretomep.txt" and move it to "YOUR FOLDER".

Histidine phosphorylation sites

You can get the source code by sending email to the Author.

Protein Function

Open the DeepGoWeb server in your browser (https://deepgo.cbrc.kaust.edu.sa/deepgo/), paste your protein sequence into the text box and submit. After the analysis, you can click "CSV Format" button to save the result. Then rename file to "deepgoweb.csv" and move it to "YOUR FOLDER".

Antigenicity, Toxicity and Allergenicity

  1. Open the VaxiJen server in your browser (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), paste your protein sequence into the text box, select a target organism "Bacteria", set threshold to "0.4" and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "vaxijen.txt" and move it to "YOUR FOLDER".
  2. Open the toxinpred 2 server in your browser (https://webs.iiitd.edu.in/raghava/toxinpred2/batch.html), paste your protein sequence into the text box, choose "AAC based RF", set threshold value to "0.6" and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "toxinpred.txt" and move it to "YOUR FOLDER".
  3. Open the AllerTop v2.0 server in your browser (https://www.ddg-pharmfac.net/AllerTOP/), paste your protein sequence into the text box and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "allertop.txt" and move it to "YOUR FOLDER".

Linear B-cell epitope

Open the ABCpred server in your browser (https://webs.iiitd.edu.in/raghava/abcpred/ABC_submission.html), paste your protein sequence into the text box and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "abcpred.txt" and move it to "YOUR FOLDER".

MHC-I and MHC-II binding

  1. Open the NetMHCpan - 4.1 server in your browser (https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/), paste your protein sequence into the text box, select peptide length "8mer peptide", type Allele names "HLA-A01:01,HLA-A02:01,HLA-A03:01,HLA-A24:02,HLA-B07:02", click "Include BA predictions" and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "MHC-I.txt" and move it to "YOUR FOLDER".
  2. Open the NetMHCIIpan - 4.0 server in your browser (https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/), paste your protein sequence into the text box, set peptide length to "15", type molecules names "DRB1_0101,HLA-DPA10103-DPB10201,HLA-DQA10102-DQB10501,H-2-IAb", click "Include BA predictions" and submit. After the analysis, you can save the data according to the template provided in the compression package. Then rename file to "MHC-II.txt" and move it to "YOUR FOLDER".

Secondary Structure

Open the NetSurfP- 3.0 server in your browser (https://services.healthtech.dtu.dk/services/NetSurfP-3.0/), paste your protein sequence into the text box and submit. After the analysis, you can click export all in the top right corner and select csv format. Then rename file to "netsurfp.csv" and move it to "YOUR FOLDER".

Tertiary Structure

This part of the analysis is more complex than the other steps, you can use the colab provided by esm to make the prediction (https://colab.research.google.com/github/facebookresearch/esm/blob/main/examples/inverse_folding/notebook.ipynb), after the prediction is completed, rename the pdb file to "esmfold.pdb" and move it to "YOUR FOLDER".

Upload

You can upload your analytics data by compressing the "YOUR FOLDER" and filling in the information at the top of the page. Please note that the maximum upload size is limited to 10M. Thank you for your contribution.

Supplement

Template sturcture

./pipeline-template/
├── abcpred.txt
├── ABL02941.1.fasta
├── allertop.txt
├── deepgoweb.csv
├── esmfold.pdb
├── MHC-I.txt
├── MHC-II.txt
├── netsurfp.csv
├── prospect.txt
├── protparam.html
├── protscale.gif
├── protscale.html
├── secretomep.txt
├── signalp.zip
├── tbpred.txt
├── tmhmm.txt
├── toxinpred.txt
└── vaxijen.txt