Experimental Study of Potential CD8⁺ Trivalent Synthetic Peptides for Liver Cancer Vaccine Development Using Sprague Dawley Rat Models

Table 1

List of databases/servers used in the research work for the screening of liver cancer proteins and prediction of epitopes.

Sr. #	Tools/servers/databases	Purpose	Web links	References
1	Human Protein Atlas	Human cancer database	http://www.proteinatlas.org	[26]
2	Bioinformatics and Research Computing	For protein comparisons	http://jura.wi.mit.edu/bioc/tools/compare.php	[66]
3	UniProtKB (UniProt Knowledgebase)	Protein database	https://www.uniprot.org/	[67]
4	CELLO	Subcellular localization prediction	http://cello.life.nctu.edu.tw/	[28]
5	VaxiJen 2.0	Antigenicity prediction	http://www.ddghttp://pharmfac.net/vaxijen/VaxiJen/VaxiJen.html	[32]
6	ANTIGENpro	—	http://scratch.proteomics.ics.uci.edu/explanation.html	[68]
7	Immunomedicine Group	—	http://imed.med.ucm.es/Tools/antigenic.html	—
8	CamSol	Solubility prediction	http://www-vendruscolo.ch.cam.ac.uk/camsolmethod.html	[69]
9	SOLpro	—	http://scratch.proteomics.ics.uci.edu/explanation.html#SOLpro	[70]
10	PROSO	—	http://mbiljj45.bio.med.uni-muenchen.de:8888/proso/proso.seam	[69]
11	Immune Epitope Database (IEDB)	Epitope prediction	http://tools.iedb.org/main/	[71]
12	HLAPred		http://crdd.osdd.net/raghava/hlapred/ref.html	[72]
13	ProPred		http://crdd.osdd.net/raghava/propred1/	[73]
14	ToxinPred	Physicochemical properties	https://webs.iiitd.edu.in/raghava/toxinpred/design.php	[36]
15	ProtParam	—	https://web.expasy.org/protparam/	[74]
16	PlifePred	—	https://webs.iiitd.edu.in/raghava/plifepred/index.php	[75]
17	AllergenFP	Allergenecity prediction	http://www.ddg-pharmfac.net/AllergenFP/
18	AlgPred	—	http://crdd.osdd.net/raghava/algpred/submission.html	[76]
19	PDB (Protein Data Bank)	Protein database	http://www.rcsb.org/pdb/home/home	[77]
20	PEP-FOLD server	Epitope modeling	http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD/	[78]
21	I-TASSER	Protein modeling	https://zhanglab.ccmb.med.umich.edu/I-TASSER/	[79]
22	Molecular Operating Environment	HLA epitope binding prediction	—	—