Table 2.

Bioinformatics resources for immunoassay development. All described bioinformatics tools are categorized by the area of interest and further by the specific property that can be examined. Information is provided on the resource type, the required input, and the associated step(s) of the bioinformatics workflow (see Fig. 2). Abbreviations: AB-Seq - antibody sequence in FASTA format, C - calculation, DA - database of annotations, DP - database of predictions, N - protein name, P - prediction method, PDB - PDB ID, Seq - protein sequence in FASTA format, Str - protein structure in PDB format, UP - UniProt ID, VS - visualization. Workflow steps: I - Biomarker suitability survey, III - Epitope localization, IV - Epitope-specific antibody survey, V - Immunogenic peptide selection, VI - Error analysis. *These tools can only be utilized if a PDB entry, i.e., a protein structure, for the target exists. ** EpiPred requires the antibody structure. However, the antibody sequence is sufficient if homology modeling is used to derive a structure model from it

Area of interest	Specific property	Bioinformatic tool	Label	Input	Step	References
Biological context	Protein function	UniProtKB	DA	N, UP	I, VI	[47]
		QuickGO	DA	N, UP		[48]
		NetGO 2.0	P	Seq		[49]
	Interaction partners	STRING	DA, DP	N, UP, Seq		[50]
	Disease involvement	OMIM	DA	N		[51]
		DisGeNET	DA	N, UP		[52]
Protein origin and location	Tissue-specific expression	Expression Atlas	DA	N, UP	I, VI	[53]
		Human Protein Atlas	DA	N, UP		[54]
		Human Body Fluid Proteome	DA	N, UP, Seq		[55]
	Subcellular location	UniProtKB	DA	N, UP		[47]
		DeepLoc-2.0	P	Seq		[56]
	Extracellular vesicle localization	Vesiclepedia	DA	N		[57]
Protein structure	Molecular weight	Compute pI/MW	C	UP, Seq	I, IV, V, VI	[58]
	Solved protein structure	Protein Data Bank*	DA	N, UP, Seq, PDB		[59, 60]
	Homology modeling	SWISS-MODEL (Repository)	P, DP	UP, Seq		[61, 62]
	Predicted protein structure	AlphaFold Protein Structure Database	DP	N, UP		[63, 64]
	Structure viewer	Mol* (Mol star)*	VS	PDB, Str		[65]
	Structural protein features	PredictProtein	P	Seq		[66]
		NetSurfP-2.0	P	Seq		[67]
		DescribePROT	DP	UP, Seq		[68]
	Disorder	DisProt	DA	N, UP		[69]
		MobiDB	DA, DP	N, UP		[70]
		IUPred3	P	UP, Seq		[71]
Proteoform complexity	Isoforms and cleavage products	UniProtKB	DA	N, UP	I, IV, V, VI	[47]
	Post-translational modifications	PhosphoSitePlus	DA	N, UP		[72]
		iPTMnet	DA	N, UP		[73]
		MusiteDeep	P	Seq		[74]
Protein interactions	Interacting residues	PredictProtein	P	Seq	IV, V, VI	[66]
		DescribePROT	DP	UP, Seq		[68]
		HybridPBRpred	P	Seq		[75]
		ANCHOR2	P	UP, Seq		[76]
		InterPro	DA	N, UP, Seq		[77]
		MobiDB	DA, DP	N, UP		[70]
	Aggregation	Aggrescan3D 2.0*	P	PDB, Str		[78]
		PASTA 2.0	P	Seq		[79]
		AmyPro	DA	N, UP, Seq		[80]
Epitopes	Epitope prediction	BepiPred-2.0	P	Seq	III, IV, V,VI	[81]
		SeRenDIP-CE	P	Seq		[82]
		ElliPro*	P	PDB, Str		[83]
		epitope3D*	P	PDB, Str		[84]
	Antibody-specific epitope prediction	EpiPred*	P	PDB, Str, AB-Seq**		[85, 86]
	Known epitopes	IEDB	DA	N, UP		[87]
		SAbDab*	DA	N, PDB		[88]
	Epitope specificity	BLAST	C	Seq		[89]