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References from Therapeutic peptide informatics in the artificial intelligence era: From curated resources to generative design. Local targets link to admitted publications; unresolved targets remain external evidence.
Therapeutic peptides: current applications and future directions
10.1038/s41392-022-00904-4 · 2022 · External reference
Clinical trial cycle times continue to increase despite industry efforts
10.1038/nrd.2017.21 · 2017 · External reference
Therapeutic peptides: recent advances in discovery, synthesis, and clinical translation
10.3390/ijms26115131 · 2025 · External reference
Trends in peptide drug discovery
10.1038/s41573-020-00135-8 · 2021 · External reference
Advance in peptide-based drug development: delivery platforms, therapeutics and vaccines
10.1038/s41392-024-02107-5 · 2025 · External reference
Peptide therapeutics: current status and future directions
10.1016/j.drudis.2014.10.003 · 2015 · External reference
Discovery of the once-weekly glucagon-like peptide-1 (GLP-1) analogue semaglutide
10.1021/acs.jmedchem.5b00726 · 2015 · External reference
Transcellular stomach absorption of a derivatized glucagon-like peptide-1 receptor agonist
10.1126/scitranslmed.aar7047 · 2018 · External reference
Early engineering approaches to improve peptide developability and manufacturability
10.1208/s12248-014-9681-9 · 2015 · External reference
Octreotide long-acting release (LAR): a review of its use in the management of acromegaly
10.2165/00003495-200363220-00014 · 2003 · External reference
Linaclotide, through activation of guanylate cyclase C, acts locally in the gastrointestinal tract to elicit enhanced intestinal secretion and transit
10.1016/j.ejphar.2010.09.019 · 2010 · External reference
Pharmacologic properties, metabolism, and disposition of linaclotide, a novel therapeutic peptide approved for the treatment of irritable bowel syndrome with constipation and chronic idiopathic constipation
10.1124/jpet.112.199430 · 2013 · External reference
DDAVP in the treatment of central diabetes insipidus
10.1056/nejm197603042941001 · 1976 · External reference
An extracellular residue determines the agonist specificity of V2 vasopressin receptors
10.1016/0014-5793(95)00150-8 · 1995 · External reference
Deep learning for advancing peptide drug development: tools and methods in structure prediction and design
10.1016/j.ejmech.2024.116262 · 2024 · External reference
Machine intelligence in peptide therapeutics: a next-generation tool for rapid disease screening
10.1002/med.21658 · 2020 · External reference
Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides
10.1093/bib/bbae275 · 2024 · External reference
A comprehensive dataset of therapeutic peptides on multi-function property and structure information
10.1038/s41597-025-05528-1 · 2025 · External reference
A review on antimicrobial peptides databases and the computational tools
2022 · External reference
The FAIR Guiding Principles for scientific data management and stewardship
10.1038/sdata.2016.18 · 2016 · External reference
Physicochemical and formulation developability assessment for therapeutic peptide delivery—a primer
10.1208/s12248-014-9688-2 · 2015 · External reference
Principles of early drug discovery
10.1111/j.1476-5381.2010.01127.x · 2011 · External reference
Deep learning in the discovery of antiviral peptides and peptidomimetics: databases and prediction tools
10.1007/s11030-025-11173-y · 2025 · External reference
AI-driven discovery of antimicrobial peptides and derivatives: database and tools
10.37349/eds.2026.1008161 · 2026 · External reference
Trends in GPCR drug discovery: new agents, targets and indications
10.1038/nrd.2017.178 · 2017 · External reference
Machine-learning-guided peptide drug discovery: development of GLP-1 receptor agonists with improved drug properties
10.1021/acs.jmedchem.4c00417 · 2024 · External reference
APD6: the antimicrobial peptide database is expanded to promote research and development by deploying an unprecedented information pipeline
10.1093/nar/gkaf860 · 2026 · External reference
CAMPR4: a database of natural and synthetic antimicrobial peptides
10.1093/nar/gkac933 · 2023 · External reference
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics
10.1093/nar/gkaa991 · 2021 · External reference
DRAMP 4.0: an open-access data repository dedicated to the clinical translation of antimicrobial peptides
10.1093/nar/gkae1046 · 2025 · External reference
dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era
10.1093/nar/gkae1019 · 2025 · External reference
SATPdb: a database of structurally annotated therapeutic peptides
10.1093/nar/gkv1114 · 2016 · External reference
10.1093/database/bay038
10.1093/database/bay038 · External reference
PepTherDia: database and structural composition analysis of approved peptide therapeutics and diagnostics
10.1016/j.drudis.2021.02.019 · 2021 · External reference
YADAMP: yet another database of antimicrobial peptides
10.1016/j.ijantimicag.2011.12.003 · 2012 · External reference
Cppsite 2.0: an available database of experimentally validated cell-penetrating peptides predicting their secondary and tertiary structures
10.1016/j.jmb.2020.11.002 · 2021 · External reference
10.1021/acs.chemrestox.5c00322
10.1021/acs.chemrestox.5c00322 · External reference
CancerPPD2: an updated repository of anticancer peptides and proteins
2025 · External reference
TumorHoPe2: an updated database for tumor homing peptides
2025 · External reference
AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses
10.1093/nar/gkt1191 · 2014 · External reference
DRAVP 2.0: a curated and genomically annotated database of antiviral peptides and proteins
10.1016/j.jmb.2026.169628 · 2026 · External reference
A database of anti-coronavirus peptides
10.1038/s41597-022-01394-3 · 2022 · External reference
FermFooDb: a database of bioactive peptides derived from fermented foods
10.1016/j.heliyon.2021.e06668 · 2021 · External reference
BioPepDB: an integrated data platform for food-derived bioactive peptides
10.1080/09637486.2018.1446916 · 2018 · External reference
PlantPepDB: a manually curated plant peptide database
10.1038/s41598-020-59165-2 · 2020 · External reference
Bioactive milk peptides: an updated comprehensive overview and database
10.1080/10408398.2023.2240396 · 2024 · External reference
THPdb2: compilation of FDA approved therapeutic peptides and proteins
10.1016/j.drudis.2024.104047 · 2024 · External reference
HIPdb: a database of experimentally validated HIV inhibiting peptides
10.1371/journal.pone.0054908 · 2013 · External reference
AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides
10.1093/nar/gku1141 · 2015 · External reference
AntiTbPdb: a knowledgebase of anti-tubercular peptides
2018 · External reference
Hmrbase2: a comprehensive database of hormones and their receptors
10.1007/s42000-023-00455-5 · 2023 · External reference
HORDB 2.0: a comprehensive dataset of peptide hormones
10.1038/s41597-026-07514-7 · 2026 · External reference
DADP: the database of anuran defense peptides
10.1093/bioinformatics/bts141 · 2012 · External reference
BaAMPs: the database of biofilm-active antimicrobial peptides
10.1080/08927014.2015.1021340 · 2015 · External reference
The EROP-Moscow oligopeptide database
10.1093/nar/gkj008 · 2006 · External reference
LAMP2: a major update of the database linking antimicrobial peptides
2020 · External reference
NeuroPedia: neuropeptide database and spectral library
10.1093/bioinformatics/btr445 · 2011 · External reference
BioDADPep: a bioinformatics database for anti-diabetic peptides
10.6026/97320630015780 · 2019 · External reference
Brainpeps: the blood–brain barrier peptide database
10.1007/s00429-011-0375-0 · 2012 · External reference
B3Pdb: an archive of blood-brain barrier-penetrating peptides
10.1007/s00429-021-02341-5 · 2021 · External reference
ConoServer: updated content, knowledge and discovery tools in the conopeptide database
10.1093/nar/gkr886 · 2012 · External reference
Kalium 3.0 is a comprehensive depository of natural, artificial, and labeled polypeptides acting on potassium channels
10.1002/pro.4776 · 2023 · External reference
NavDB: a comprehensive database for voltage-gated sodium channels modulators and targets
10.1021/acs.jcim.5c02124 · 2026 · External reference
CycPeptMPDB: a comprehensive database of membrane permeability of cyclic peptides
10.1021/acs.jcim.2c01573 · 2023 · External reference
The Immune Epitope Database (IEDB): 2024 update
10.1093/nar/gkae1092 · 2025 · External reference
AntiBP3: a method for predicting antibacterial peptides against gram-positive/negative/variable bacteria
10.3390/antibiotics13020168 · 2024 · External reference
iAMP-2L: a two-level multi-label classifier for identifying antimicrobial peptides and their functional types
10.1016/j.ab.2013.01.019 · 2013 · External reference
Deep-ABPpred: identifying antibacterial peptides in protein sequences using bidirectional LSTM with word2vec
10.1093/bib/bbab065 · 2021 · External reference
Meta-iAVP: a sequence-based meta-predictor for improving the prediction of antiviral peptides using effective feature representation
10.3390/ijms20225743 · 2019 · External reference
ACVPICPred: inhibitory activity prediction of anti-coronavirus peptides based on artificial neural network
10.1016/j.csbj.2024.09.015 · 2024 · External reference
AntiCP 2.0: an updated model for predicting anticancer peptides
10.1093/bib/bbaa153 · 2021 · External reference
CD47Binder: identify CD47 binding peptides by combining next-generation phage display data and multiple peptide descriptors
10.1007/s12539-023-00575-x · 2023 · External reference
PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning
10.1093/bioinformatics/btz246 · 2019 · External reference
MCMFPP: a multifunctional peptides prediction method based on class feature enhancement and classifier fusion
10.1021/acs.jcim.5c01693 · 2025 · External reference
modlAMP: Python for antimicrobial peptides
10.1093/bioinformatics/btx285 · 2017 · External reference
PeptideBERT: a language model based on transformers for peptide property prediction
10.1021/acs.jpclett.3c02398 · 2023 · External reference
Multi-peptide: multimodality leveraged language-graph learning of peptide properties
10.1021/acs.jcim.4c01443 · 2025 · External reference
10.1093/nar/gkz321
10.1093/nar/gkz321 · External reference
PASTA 2.0: an improved server for protein aggregation prediction
10.1093/nar/gku399 · 2014 · External reference
ToxinPred2: an improved method for predicting toxicity of proteins
10.1093/bib/bbac174 · 2022 · External reference
HyPepTox-Fuse: an interpretable hybrid framework for accurate peptide toxicity prediction fusing protein language model-based embeddings with conventional descriptors
10.1016/j.jpha.2025.101410 · 2025 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER
10.1038/s41587-025-02654-4 · 2026 · External reference
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex
10.1093/nar/gkw329 · 2016 · External reference
LAMMPS – a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
10.1016/j.cpc.2021.108171 · 2022 · External reference
GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers
10.1016/j.softx.2015.06.001 · 2015 · External reference
AmberTools
10.1021/acs.jcim.3c01153 · 2023 · External reference
Recent developments in Amber Biomolecular Simulations
10.1021/acs.jcim.5c01063 · 2025 · External reference
Robust deep learning-based protein sequence design using ProteinMPNN
10.1126/science.add2187 · 2022 · External reference
De novo design of protein structure and function with RFdiffusion
10.1038/s41586-023-06415-8 · 2023 · External reference
Target sequence-conditioned design of peptide binders using masked language modeling
10.1038/s41587-025-02761-2 · 2026 · External reference
Generative latent diffusion language modeling yields anti-infective synthetic peptides
10.1016/j.celbio.2025.100183 · 2025 · External reference
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
10.1038/s41596-024-01011-0 · 2024 · External reference
HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm
10.1093/nar/gky357 · 2018 · External reference
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
10.1093/nar/gkv456 · 2015 · External reference
ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides
10.1093/bioinformatics/bty451 · 2018 · External reference
MLACP: machine-learning-based prediction of anticancer peptides
10.18632/oncotarget.20365 · 2017 · External reference
mACPpred: a support vector machine-based meta-predictor for identification of anticancer peptides
10.3390/ijms20081964 · 2019 · External reference
MLACP 2.0: an updated machine learning tool for anticancer peptide prediction. Comput Struct
2022 · External reference
mACPpred 2.0: stacked deep learning for anticancer peptide prediction with integrated spatial and probabilistic feature representations
10.1016/j.jmb.2024.168687 · 2024 · External reference
AIPpred: sequence-based prediction of anti-inflammatory peptides using random forest
10.3389/fphar.2018.00276 · 2018 · External reference
Machine-learning-based prediction of cell-penetrating peptides and their uptake efficiency with improved accuracy
10.1021/acs.jproteome.8b00148 · 2018 · External reference
MLCPP 2.0: an updated cell-penetrating peptides and their uptake efficiency predictor
10.1016/j.jmb.2022.167604 · 2022 · External reference
StackDPPIV: a novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides
10.1016/j.ymeth.2021.12.001 · 2022 · External reference
B3Pred: a random-forest-based method for predicting and designing blood-brain barrier penetrating peptides
10.3390/pharmaceutics13081237 · 2021 · External reference
BBPpredict: a web service for identifying blood-brain barrier penetrating peptides
2022 · External reference
Prediction of blood-brain barrier penetrating peptides based on data augmentation with Augur
10.1186/s12915-024-01883-4 · 2024 · External reference
DeepB3P: a transformer-based model for identifying blood-brain barrier penetrating peptides with data augmentation using feedback GAN
10.1016/j.jare.2024.08.002 · 2025 · External reference
iCTX-Type: a sequence-based predictor for identifying the types of conotoxins in targeting ion channels
10.1155/2014/286419 · 2014 · External reference
STACKION: ion channel-modulating peptides identification using stacking-based ensemble machine learning
2023 · External reference
A PLM-based method for predicting protein ion channel modulators for drug discovery and safety evaluation
10.1002/pro.70689 · 2026 · External reference
pepADMET: a novel computational platform for systematic ADMET evaluation of peptides
10.1021/acs.jcim.5c02518 · 2026 · External reference
ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support
10.1093/nar/gkae236 · 2024 · External reference
Unresolved reference
External reference
Prediction of cell-penetrating potential of modified peptides containing natural and chemically modified residues
10.3389/fmicb.2018.00725 · 2018 · External reference
An ensemble method for predicting and designing of druggable proteins
10.1002/prca.70046 · 2026 · External reference
A large language model for predicting neurotoxic peptides and neurotoxins
10.1002/pro.70200 · 2025 · External reference
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data
10.1093/nar/gkaa379 · 2020 · External reference
Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning
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AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes
10.1093/bib/bbaa294 · 2021 · External reference
PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues
10.1186/s13062-015-0103-4 · 2015 · External reference
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints
2024 · External reference
Cyclic peptide structure prediction and design using AlphaFold2
10.1038/s41467-025-59940-7 · 2025 · External reference
NCPepFold: accurate prediction of noncanonical cyclic peptide structures via cyclization optimization with multigranular representation
10.1021/acs.jctc.5c00139 · 2025 · External reference
Instruction multi-constraint molecular generation using a teacher-student large language model
2024 · External reference
The I-TASSER Suite: protein structure and function prediction
10.1038/nmeth.3213 · 2015 · External reference
Swiss-MODEL: homology modelling of protein structures and complexes
10.1093/nar/gky427 · 2018 · External reference
Conotoxins targeting voltage-gated sodium ion channels
10.1124/pharmrev.123.000923 · 2024 · External reference
Scorpion peptides and ion channels: an insightful review of mechanisms and drug development
10.3390/toxins15040238 · 2023 · External reference
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Revisiting ADMET prediction reliability under real-world challenges in the foundation model era
10.1186/s13321-026-01217-2 · 2026 · External reference
An end-user audit of reproducibility, data leakage, and overfitting of the top-ranked ADMET prediction models in TDC leaderboards
10.1021/acs.jcim.6c00819 · 2026 · External reference
HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation
10.1093/bioinformatics/btaa160 · 2020 · External reference
Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3
10.1093/bib/bbaf488 · 2025 · External reference
