Table 5 Common in-silico databases reported in the literature

Protein/peptide sequence databases

BIOPEP

http://www.uwm.edu.pl/biochemia/index.php/en/biopep

Protein and peptide database

Agyei et al. (2016); Cárdenas et al. (2020); De La Fuente et al. (2021); Senadheera et al. (2022); Tu et al. (2018); Vilas Boas et al. (2019)

PepBank

http://pepbank.mgh.harvard.edu/

Peptide database

BioPD

http://biopd.bjmu.edu.cn/

Peptide database

SwePep

http://www.swepep.org/

Sweden peptide database

EROP-Moscow

http://erop.inbi.ras.ru/

Peptide database

MilkAMP

http://milkampdb.org/home.php

Dairy antimicrobial peptide database

UniProtKB

http://www.uniprot.org/

Primary sequence and structural information for proteins

NCBI Protein database

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

Basic sequence information for proteins

PeptideDB

http://www.peptides.be/

Peptide database

AVPdb

http://crdd.osdd.net/servers/avpdb/index.php

Database of anti-viral peptides

CAMPR3

http://www.camp.bicnirrh.res.in/

Collection of anti-microbial peptides

HIPdb

http://crdd.osdd.net/servers/hipdb/index.php

Database of HIV inhibiting peptides

BACTIBASE

http://bactibase.hammamilab.org/main.php

Database of bacteriocins

APD

https://wangapd3.com/main.php

Antimicrobial peptide database

http://aps.unmc.edu/AP/

BitterDB

http://bitterdb.agri.huji.ac.il/dbbitter.php

Database for bitter peptides

In silico digestion Tools

BIOPEP

http://www.uwm.edu.pl/biochemia/index.php/en/biopep

Tools for peptide predication

PeptideCutter

http://web.expasy.org/peptide cutter/

Predict peptide cleavage sites

POPS

http://pops.csse.monash.edu.au/pops-cgi/index.php

Tool for modelling and predicting protease specificity

http://www.mybiosoftware.com/pops-2-1-1-prediction-protease-specificity.html

NeuroPred

http://stagbeetle.animal.uiuc.edu/cgi-bin/neuropred.py

Prediction of cleavage sites and mass from neuropeptide precursors

CAMPSign

http://www.campsign.bicnirrh.res.in/

Identification of AMPs using AMP family signatures

Enzyme Predictor

http://bioware.ucd.ie/~enzpred/Enzpred.php

Evaluation tool to determine the cleavage ability of enzymes

Potential bioactivity prediction

PeptideRanker

http://bioware.ucd.ie/∼compass/biowareweb/

Pediction of bioactive peptides

BIOPEP

http://www.uwm.edu.pl/biochemia/index.php/en/biopep

Pediction of bioactive peptides

AntiBP2

http://www.imtech.res.in/raghava/antibp2/

Antibacterial peptide prediction tool

AVPpred

http://crdd.osdd.net/servers/avppred/submit.php

Collection and prediction of antiviral peptides

AVP-IC50Pred

http://crdd.osdd.net/servers/ic50avp/index.html

Prediction of peptide antiviral activity in terms of IC₅₀

Toxicity/allergenicity prediction

ToxinPred

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

Predicting the toxicity of peptides

BIOPEP

http://www.uwm.edu.pl/biochemia/index.php/en/biopep

Allergenic protein database

AlgPred

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

Predicting allergenic proteins and peptides

Allerdictor

https://openebench.bsc.es/tool/allerdictor

Allergen prediction tool

EPIMHC

http://bio.med.ucm.es/epimhc/

Database of Naturally Processed MHC-restricted Peptide Ligands and Epitopes for Customized Computational Vaccinology

Physicochemical characteristics prediction

Expasy-Compute pI/Mw

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

A tool to compute the theoretical pI (isoelectric point) and MW (mol weight)

ProtParam

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

A tool to compute the grand average of hydropathicity (GRAVY) and Instability index

Peptide Structure Prediction Server

PepDraw

http://www.tulane.edu/~biochem/WW/PepDraw/

A tool to compute net charge and hydrophobicity

Pep-Fold

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

Predicting peptide structures from amino acid sequences

PEPstrMOD

http://osddlinux.osdd.net/raghava/pepstrmod/

Predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues

I-TASSER

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

Protein structure prediction and structure-based function annotation