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

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]