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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]