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Table 1 Tools, Databases and Software used in this study

From: Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors

Database/Tools

Web Link

Purpose

References

NCBI

https://www.ncbi.nlm.nih.gov/

Accession of Data

–

T2D@ZJU

http://pharminfo.zju.edu.cn/t2d

Diabetes associated genes retrieval

[18]

DAPD

http://mkarthikeyan.bioinfoau.org/dapd/

Retrieval of proteins

[19]

ToxinPred & PredSTP

https://webs.iiitd.edu.in/raghava/toxinpred/index.html

Prediction of toxic peptides

[20, 21]

UniProt

http://www.uniprot.org

Screening of Diabetic proteins

[22]

Compare Two Lists

http://jura.wi.mit.edu/bioc/tools/compare.php

Comparison

[23].

SPpred

http://crdd.osdd.net:8081/sppred/submit.jsp

Solubility/hydrophilicity determination

–

PROTPARAM

http://web.expasy.org/protparam/

Amino Acid composition

[24]

CELLO

http://cello.life.nctu.edu.tw/

Subcellular Localization Prediction

[25]

PROPRED I

http://crdd.osdd.net/raghava/propred1/

Prediction of T-Cell epitopes

[24]

HADDOCK 2.2

https://haddock.science.uu.nl/

Docking of epitopes

[26]

IEDB (NetChop)

http://tools.iedb.org/netchop/result/

Proteasomal cleavage prediction

[27].

IEDB

http://tools.iedb.org/conservancy/

Epitope Conservancy Analysis

[28]

PEPFOLD

http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/

3D Modelling of Epitopes

[29]

DAVID Tool

https://david.ncifcrf.gov/home.jsp

Functional Annotation

[30]

HAPPI

http://discovery.informatics.uab.edu/HAPPI/

Interactomic analysis

[31]

STRING

https://string-db.org/

Interactomic analysis

[32].

Cytoscape

http://www.cytoscape.org/

Protein-protein interaction

[33]

MOE

https://www.chemcomp.com/

Epitopes binding energy

–

ITASSER

https://zhanglab.ccmb.med.umich.edu/I-TASSER/

3D Model generation

[34,35,36]

Chimera

https://www.cgl.ucsf.edu/chimera/

Visualization of proteins

[37]

FUNRICH

http://www.funrich.org/

Gene enrichment analysis

[38]

ERRAT

http://servicesn.mbi.ucla.edu/ERRAT/

Error in model estimation

[39]

QMean

https://swissmodel.expasy.org/qmean/

Quality of model

[40, 41]

Rampage Analysis

http://mordred.bioc.cam.ac.uk/~rapper/rampage.php

Protein Quality

[42]

3D Refine

http://sysbio.rnet.missouri.edu/3Drefine/

Refinement of polyvalent model

[43,44,45]

Antigen Pro

http://scratch.proteomics.ics.uci.edu/

Antigenicity

[46]

Vaxijen

http://www.ddg-pharmfac.net/vaxijen/VaxiJen/

Antigenicity

[47,48,49]

AlgPred

http://crdd.osdd.net/raghava/algpred/submission.html

Allergenicity

–

Sol Pro

http://scratch.proteomics.ics.uci.edu/explanation.html#SOLpro

Solubility of proteins

[46]

Expasy

http://web.expasy.org/compute_pi/

Molecular Weight prediction

[24]