Explore studies of cell penetrating.
MCoTI-II was internalized into human cells through macropinocytosis (not receptor-mediated endocytosis), accumulating in cytoplasm — demonstrating that macrocyclic peptide scaffolds can access intracellular targets, dramatically expanding their drug design utility.
Greenwood, Kathryn P; Daly, Norelle L; Brown, Darren L; Stow, Jennifer L; Craik, David J · In Vitro
Cell-permeable antioxidant peptide (SS-31 family) reduced renal tubular apoptosis, oxidative damage, and fibrosis in unilateral ureteral obstruction rats — expanding mitochondria-targeted peptide therapy to kidney protection for obstructive and other renal diseases.
Mizuguchi, Yasunori; Chen, Jie; Seshan, Surya V; Poppas, Dix P; Szeto, Hazel H; Felsen, Diane · Animal Study
The cell-penetrating peptide (CPP) was the key ingredient. Without CPP, the PLGA nanoparticles carrying plasmid DNA showed minimal cell uptake. With CPP attached, 84% of Beas-2B cells and 97% of A549 lung cancer cells internalized the nanoparticles within just 3 hours. The particles entered cells mainly through clathrin-mediated endocytosis, a common cellular intake pathway. Once inside, the particles appeared to escape the endosome compartment, which is critical for the DNA cargo to reach its target. The delivered DNA produced green fluorescent protein (eGFP) in Beas-2B cells after 96 hours, confirming functional gene delivery. The nanoparticles released about 50% of their DNA cargo in the first 24 hours, with encapsulation efficiency high enough to be practical.
Gomes Dos Reis, Larissa; Lee, Wing-Hin; Svolos, Maree; Moir, Lyn M; Jaber, Rima; Engel, Andrea; Windhab, Norbert; Young, Paul M; Traini, Daniela · In Vitro (Cell Culture)
The core problem: cell-penetrating peptides (CPPs) have positive charges that can interfere with the function of attached cargo peptides inside cells. Direct conjugation often does not work reliably. The solution: an 8-unit PNA sequence conjugated to octa-arginine CPP (PNA1-CPP) paired with a complementary PNA attached to an autophagy-inducing peptide (PNA2-AIP). The two PNA strands hybridized, forming a stable 1:1 complex that kept the functional peptide connected to the CPP during delivery. Once inside cells, at least some of the PNA1-CPP/PNA2-AIP complexes dissociated, releasing the functional AIP from the positively charged CPP. The released PNA2-AIP induced significantly more autophagy than AIP directly conjugated to CPP (CPP-AIP). The PNA hybrid system also caused minimal cell death.
Hakata, Yoshiyuki; Ishikawa, Suzuka; Ohtsuki, Takashi; Miyazawa, Masaaki; Kitamatsu, Mizuki · In Vitro (Proof Of Concept)
The researchers created peptide dendrimer variants carrying fluorescent labels in their core. These labeled versions maintained the same siRNA transfection efficiency, pH-dependent aggregation, siRNA binding, and secondary structures as unlabeled dendrimers. FRET (fluorescence resonance energy transfer) experiments revealed the delivery mechanism in detail: at pH 7.4 (normal cellular pH), dendrimers and siRNA are tightly packed together in nanoparticles. At pH 5.0 (endosomal pH), the complex loosens and dendrimers are released into solution. At this acidic pH, the dendrimers destabilize endosomal membranes, enabling escape into the cytoplasm where siRNA can silence target genes. Colocalization studies showed dendrimers and siRNA stay together throughout the uptake process, separating only after reaching acidic endosomes. This pH-triggered release mechanism is what makes the system effective.
Heitz, Marc; Zamolo, Susanna; Javor, Sacha; Reymond, Jean-Louis · In Vitro (Mechanistic)
A systematic computational screen of the SARS-CoV-2 proteome identified 310 sequences with cell-penetrating peptide (CPP) characteristics. These SCV2-CPPs spanned regions involved in replication, protein-nucleotide interaction, protein-protein interaction, and complex stabilization. Safety and practicality analysis: 94.3% were predicted non-toxic. 38% were neither antigenic nor allergenic, important for therapeutic use. 36.7% resisted all four major protease families, meaning they could survive in biological fluids. Structural analysis: about one-third had sufficient helix or sheet structure for efficient cellular uptake. Among helical CPPs, 44.3% were predicted lipid-binding, important for membrane interaction. The top candidates for drug delivery were SCV2-CPP118, 119, 122, and 129, all from NSP12 (RNA-dependent RNA polymerase). Cysteine-rich CPPs from the helicase (NSP13) could potentially form cyclic structures in endosomes for better release. Beyond delivery: 59.6% had predicted antibacterial activity, 29.6% antiviral, 32.3% antifungal, 63.6% immunomodulatory, and 21.9% anticancer properties.
Hemmati, Shiva; Behzadipour, Yasaman; Haddad, Mahdi · Computational/Bioinformatics
Two series of hybrid gamma/gamma-peptides (gamma-CC and gamma-CT) were designed using a chiral cyclobutane amino acid alternating with proline derivatives. Key findings: Selectivity: both peptide series showed no cytotoxicity to human HeLa cells and only moderate uptake by these cells. In contrast, both 14-mer versions were microbicidal against Leishmania at concentrations above 25 micromolar, with significant intracellular accumulation in the parasite. Drug delivery: when conjugated to fluorescent doxorubicin (Dox), the peptides showed toxicity to Leishmania above 1 micromolar, while free Dox at the same concentration was not toxic. Intracellular accumulation was 2.5 times higher than with a Dox-TAT conjugate (TAT being the standard cell-penetrating peptide). Structural insight: computational calculations showed the drug-peptide conjugates fold to bury the Dox moiety inside a cavity while exposing positively charged groups to solvent. This improves Dox solubility and membrane translocation.
Illa, Ona; Olivares, José-Antonio; Gaztelumendi, Nerea; Martínez-Castro, Laura; Ospina, Jimena; Abengozar, María-Ángeles; Sciortino, Giuseppe; Maréchal, Jean-Didier; Nogués, Carme; Royo, Míriam; Rivas, Luis; Ortuño, Rosa M · In Vitro (Peptide Design + Parasitology)
The K10H16 fusion peptide delivers functional enzymes to intracellular lysosomes via electrostatic complexation, restoring normal cell growth in lysosomal storage disease cells.
Iwasaki, Takashi; Murakami, Nodoka; Kawano, Tsuyoshi · In Vitro (Proof Of Concept)
Triple-peptide pH-responsive nanoparticles co-delivering irinotecan and miR-200 outperformed Onivyde in a head and neck cancer mouse model by simultaneously targeting EMT, MDR, and Wnt pathways.
Lo, Yu-Li; Chang, Chih-Hsien; Wang, Chen-Shen; Yang, Muh-Hwa; Lin, Anya Maan-Yuh; Hong, Ci-Jheng; Tseng, Wei-Hsuan · Animal
Peptide-based nanoformulations can enhance cancer treatment efficacy by improving tumor penetration, increasing circulation time, and reducing off-target toxicity when combined with conventional therapies.
Mehrotra, Neha; Kharbanda, Surender; Singh, Harpal · Review
Ara-27 achieved >99% cell-penetrating efficiency at 2 μM in human cells compared to <10% for Tat-PTD and MTS, with 8-22x higher intracellular fluorescence intensity.
Min, Sol; Kim, Kichul; Ku, Seockmo; Park, Jeong-Yoon; Seo, Jeongmin; Roh, Sangho · In Vitro
Hydrophobic amino acid linkers (FF and LL) adjacent to the photosensitizer significantly enhanced photochemical internalization efficiency in CPP-cargo-PS conjugates across multiple cargo types.
Miyoshi, Yuichi; Kadono, Maho; Okazaki, Shigetoshi; Nishimura, Ayano; Kitamatsu, Mizuki; Watanabe, Kazunori; Ohtsuki, Takashi · In Vitro
SialoPen peptides — de novo designed foldamers using a Neu2en scaffold — demonstrated significantly superior cellular uptake compared to classical CPPs penetratin and HIV-TAT in both HeLa and neuronal cells.
Monreal, I Abrrey; Contreras, Erik M; Wayman, Gary A; Aguilar, Hector C; Saludes, Jonel P · In Vitro
The cyclic cLK peptide delivered fragmented Runx2 into stem cells more efficiently than Tat-CPP, producing 1.2-fold greater mineralization and higher osteogenic gene expression.
Nam, So Hee; Lee, Yan; Ahn, Joon Hyung; Chung, Chun Kee; Yang, Hee-Jin; Park, Sung Bae; Jang, Sangmok · In Vitro
Anti-ftsZ PNAs completely inhibited E. faecalis growth, while CPP-conjugated anti-efaA PNAs reduced efaA gene expression and biofilm formation by 95%, with no mammalian cell toxicity.
Narenji, Hanar; Teymournejad, Omid; Rezaee, Mohammad Ahangarzadeh; Taghizadeh, Sepehr; Mehramuz, Bahareh; Aghazadeh, Mohammad; Asgharzadeh, Mohammad; Madhi, Masoumeh; Gholizadeh, Pourya; Ganbarov, Khudaverdi; Yousefi, Mehdi; Pakravan, Asrin; Dal, Tuba; Ahmadi, Raman; Samadi Kafil, Hossein · In Vitro
CPP-conjugated PNAs and siRNAs can inhibit hepatitis B virus replication and antigen expression, with CPPs solving the critical intracellular delivery challenge for oligonucleotide-based antivirals.
Ndeboko, Bénédicte; Omouessi, Serge Thierry; Ongali, Brice; Mouinga-Ondémé, Augustin · Review
Active NBD peptide reduced albuminuria by >40%, decreased podocyte loss and basement membrane thickness, and modulated inflammatory markers in a type 2 diabetic nephropathy mouse model.
Opazo-Ríos, Lucas; Plaza, Anita; Sánchez Matus, Yenniffer; Bernal, Susana; Lopez-Sanz, Laura; Jimenez-Castilla, Luna; Carpio, Daniel; Droguett, Alejandra; Mezzano, Sergio; Egido, Jesús; Gomez-Guerrero, Carmen · Animal Study
PAS-pHK peptide delivers miR-126 selectively to cancer cells, targeting mitochondria to induce apoptosis synergistically while showing no toxicity to non-cancerous cells.
Palanikumar, L; Al-Hosani, Sumaya; Kalmouni, Mona; Saleh, Hadi Omar; Magzoub, Mazin · In Vitro
All synthesized penetratin analogues demonstrated measurable trans-corneal diffusion despite their hydrophilic nature and ~1.6 kDa size, though none achieved the penetration efficiency of full-length penetratin.
Pescina, Silvia; Sala, Marina; Scala, Maria Carmina; Santi, Patrizia; Padula, Cristina; Campiglia, Pietro; Ostacolo, Carmine; Nicoli, Sara · In Vitro
Smac-CPP nanoparticles combined with doxorubicin reduced tumor growth by 85% in vivo, with decreased Ki-67 proliferation staining and increased cleaved caspase-3 apoptosis staining in tumors.
Priwitaningrum, Dwi L; Jentsch, Julian; Bansal, Ruchi; Rahimian, Sima; Storm, Gert; Hennink, Wim E; Prakash, Jai · Animal Study
INH-CPP conjugates showed conjugation-induced structural and membrane interaction changes that correlated with each other; Penetratin and Transportan conjugates had similar cell uptake but different subcellular localization and anti-Mtb activity.
Pári, Edit; Horváti, Kata; Bősze, Szilvia; Biri-Kovács, Beáta; Szeder, Bálint; Zsila, Ferenc; Kiss, Éva · In Vitro
TAT-FADD entered cancer cells via caveolar endocytosis, assembled DISC to trigger apoptosis, suppressed NF-κB and downstream anti-apoptotic genes (Bcl2, cFLIPL, RIP1, cIAP2), and inhibited NLRP3 inflammasome priming and IL-1β secretion.
Ranjan, Kishu; Waghela, Bhargav N; Vaidya, Foram U; Pathak, Chandramani · In Vitro
CPPs escape endosomes through a budding-and-collapse mechanism: CPP-enriched vesicles bud from the endosomal membrane and subsequently collapse, releasing cargo into the cytosol.
Sahni, Ashweta; Qian, Ziqing; Pei, Dehua · In Vitro
Smaller vesicles suppressed CPP cytolysis despite higher membrane curvature, because reduced lipid mobility in smaller vesicles restricts the local phase transitions required for CPP membrane penetration.
Sakamoto, Kazutami; Kitano, Takeshi; Kuwahara, Haruka; Tedani, Megumi; Aburai, Kenichi; Futaki, Shiroh; Abe, Masahiko; Sakai, Hideki; Ohtaka, Hiroyasu; Yamashita, Yuji · In Vitro
CPP cytolysis occurs in two steps: rapid adsorption (saturated within 10 min) followed by linear-rate internalization dependent on osmotic pressure. The mechanism involves Lα to Mesh1 lipid phase transition creating punctured bilayer morphologies.
Sakamoto, Kazutami; Morishita, Taku; Aburai, Kenichi; Sakai, Kenichi; Abe, Masahiko; Nakase, Ikuhiko; Futaki, Shiroh; Sakai, Hideki · In Vitro
tCPP conjugation achieved up to 4-fold elevated internalization rates for three clinical antibodies while retaining target specificity. tCPP-Kadcyla showed 6-fold increased cytotoxicity. Favorable pharmacokinetics limited off-target accumulation.
Sauter, Max; Strieker, Matthias; Kleist, Christian; Wischnjow, Artjom; Daniel, Volker; Altmann, Annette; Haberkorn, Uwe; Mier, Walter · In Vitro
CPPs can effectively assist nanotherapeutics in crossing cell membranes, with demonstrated applications in cancer therapy, tumor imaging, atherosclerosis evaluation, thrombin detection, and HIV therapy.
Desale, Kalyani; Kuche, Kaushik; Jain, Sanyog · Review
Peptide vector P-02 (SP-PEG4-K(C18)-(LLHH)3-R9) achieved 36% higher transfection in glioma U87 cells versus normal 293T cells, with NK1 receptor-mediated targeting confirmed. The vector crossed a BBB model in vitro and achieved gene expression in zebrafish brain.
Ding, Guihua; Wang, Taoran; Han, Zhenbin; Tian, Long; Cheng, Qin; Luo, Longlong; Zhao, Baoquan; Wang, Chenhong; Feng, Siliang; Wang, Lianshuai; Meng, Zhao; Meng, Qingbin · In Vitro + Animal (Zebrafish)
VIVIT-GFP overexpression successfully inhibited NFAT signaling in glioma cells, but neither Sim2-VIVIT nor 11R-VIVIT cell-penetrating peptide conjugates could reproduce this effect, indicating CPP delivery is insufficient for NFATc3-expressing gliomas.
Ellert-Miklaszewska, Aleksandra; Szymczyk, Agata; Poleszak, Katarzyna; Kaminska, Bozena · In Vitro
E. coli resistance to CPP-delivered antimicrobials requires constitutive Cpx stress response activation (cpx*), which decreases cytoplasmic membrane potential and blocks energy-dependent uptake of arginine-rich CPP conjugates.
Frimodt-Møller, Jakob; Koulouktsis, Andreas; Charbon, Godefroid; Otterlei, Marit; Nielsen, Peter E; Løbner-Olesen, Anders · In Vitro (Bacterial Genetics)
Iterative peptide design yielded functional peptides with refined ability to modulate biomembrane barrier function, lipid packing, and structure.
Futaki, Shiroh · Review
A novel CPP derived from CDN1 was identified through in silico screening and experimentally validated for cellular uptake and intracellular labeling in living cells.
Guo, Xiangli; Chen, Linlin; Wang, Lidan; Geng, Jingping; Wang, Tao; Hu, Jixiong; Li, Jason; Liu, Changbai; Wang, Hu · In Vitro Study
ACPP-resiquimod conjugate achieved >1,000-fold greater tumor tissue concentration than surrounding normal tissue after systemic delivery. Therapeutic efficacy matched localized free resiquimod in syngeneic murine tumors. Dual enzymatic activation: MMP-2/9 cleavage + cathepsin B release.
Hingorani, Dina V; Camargo, Maria F; Quraishi, Maryam A; Adams, Stephen R; Advani, Sunil J · Preclinical Animal Study
HNLS-3 displayed pH-dependent cellular uptake, endosomal escape, and nuclear localization. HNLS-3-CPT conjugate showed enhanced cytotoxicity and selectivity compared to free CPT.
Huang, Sujie; Zhu, Zhongwen; Jia, Bo; Zhang, Wei; Song, Jingjing · In Vitro Study
Characterized the kinetics of CPP-induced pore formation in stearoyl-oleoyl-phosphatidylcholine vesicles, providing mechanistic data for engineering endosomal escape in liposomal drug delivery.
James, Honey Priya; Jadhav, Sameer · Biophysical Study
TAT-P110 and SS-31 both reversed Drp1-dependent mitochondrial fragmentation in FRDA cells. TAT-P110 decreased ATP levels (suggesting fragmentation is homeostatic). SS-31 reversed fragmentation without affecting ATP. Both act through the same pathway with different downstream effects.
Johnson, Joseph; Mercado-Ayón, Elizabeth; Clark, Elisia; Lynch, David; Lin, Hong · In Vitro Study
Penetratin-conjugated LPNVs showed efficient cellular uptake, specific ER-targeting, and remarkable lysosomal escape due to pH buffering by PEO-b-PCL-b-PEO, enabling intracellular ER-targeted delivery.
Kang, Jeong Yi; Kim, Seulgi; Kim, Juhyeon; Kang, Nae-Gyu; Yang, Chul-Su; Min, Sun-Joon; Kim, Jin Woong · In Vitro
Six-membered carbocyclic α,α-disubstituted amino acids were synthesized and incorporated into arginine-rich CPPs. Ring size affected peptide helicity and cell-penetrating properties, providing design insights for CPP optimization.
Kato, Takuma; Kita, Yuki; Iwanari, Kazuki; Asano, Akiko; Oba, Makoto; Tanaka, Masakazu; Doi, Mitsunobu · In Vitro
Hybrid cyclic-linear CPPs with alternative positively charged and hydrophobic amino acids showed enhanced cellular uptake and delivery of cell-impermeable, negatively charged molecules.
Khayyatnejad Shoushtari, Sorour; Zoghebi, Khalid; Sajid, Muhammad Imran; Tiwari, Rakesh Kumar; Parang, Keykavous · In Vitro
AP CPP (9 amino acids with one cysteine) delivered EGFP to human T cells and biodistributed to spleen, liver, intestines, and brain after systemic administration. AP-ctCTLA-4 reduced Th17 differentiation in vitro and ameliorated EAE with decreased IL-17A+GM-CSF+ CD4 T cells in vivo.
Kim, Won-Ju; Kim, Gil-Ran; Cho, Hyun-Jung; Choi, Je-Min · Animal
The heterodimeric leucine zipper system (LzK/LzE) formed a 1:1 hybrid in solution, confirmed by fluorescence spectroscopy, effectively conjugating cargo proteins to cell-penetrating peptides without covalent modification. When used to deliver p53 (p53-LzK/LzE-CPP), the hybrid localized to cell nuclei and inhibited cell-specific proliferation across multiple cell lines. Critically, the leucine zipper delivery system outperformed the directly fused p53-CPP conjugate in proliferation inhibition, suggesting that the non-covalent, modular attachment preserves protein cargo activity better than direct fusion.
Kitamatsu, Mizuki; Yuasa, Hiroki; Ohtsuki, Takashi; Michiue, Hiroyuki · In Vitro
CPPs enhance diabetes treatment by: (1) improving hypoglycemic drug effectiveness, (2) facilitating insulin delivery, (3) synergizing with immunosuppressants for islet transplantation, (4) prolonging drug pharmacokinetics, and (5) retarding diabetic nephropathy.
Korivi, Mallikarjuna; Huang, Yue-Wern; Liu, Betty R · Review
Tachyplesin demonstrated effective anti-leishmanial activity against Leishmania donovani, the causative agent of visceral leishmaniasis, through a peptide-mediated parasite killing mechanism.
Kumar, Vivek; Chugh, Archana · In Vitro
pH cascade-responsive cRGD-targeted micellar nanoplatform achieved nucleus-targeted co-delivery of chemotherapy drug GNA002 and photodynamic therapy agent, enabling synergistic chemo-photodynamic cancer treatment.
Li, Fan; Liang, Yan; Wang, Miaochen; Xu, Xing; Zhao, Fen; Wang, Xu; Sun, Yong; Chen, Wantao · Animal
One of the biggest barriers in gene therapy is the endosomal trap. Cells engulf nanoparticles carrying therapeutic genes, but the particles get stuck inside endosomes and are destroyed before they can deliver their cargo to the cell nucleus. Melittin, a 26-amino-acid peptide from bee venom, can disrupt endosomal membranes and release the trapped cargo. However, melittin is extremely toxic to mammalian cells at normal concentrations because it also destroys the outer cell membrane. Researchers have addressed this by modifying melittin's amino acid sequence to reduce its toxicity while preserving its membrane-disrupting ability. Strategies include making pH-sensitive versions that only activate inside acidic endosomes (where the gene cargo is trapped) and conjugating melittin to nanoparticle carriers so it acts locally rather than freely.
Paray, Bilal Ahamad; Ahmad, Aqeel; Khan, Javed Masood; Taufiq, Faisal; Pathan, Aslam; Malik, Ajamaluddin; Ahmed, Mohammad Z · Review
The POSEIDON database contains over 2,300 experimental entries with quantitative uptake values (how much peptide actually entered cells) and physicochemical properties for 1,315 peptides. Using this data plus genomic features of different cell lines, the team trained a regression model. The model achieved a Pearson correlation of 0.87, Spearman correlation of 0.88, and r-squared of 0.76 on an independent test set. This means the model explains about 76% of the variation in peptide uptake across different cell types.
Preto, António J; Caniceiro, Ana B; Duarte, Francisco; Fernandes, Hugo; Ferreira, Lino; Mourão, Joana; Moreira, Irina S · Computational/Database
HNSS showed a 2-fold improvement in brain distribution compared to HNG alone. Its structure mimics cell-penetrating peptides, which explains the enhanced brain entry. Inside the brain, HNSS worked on multiple fronts. It targeted mitochondria and scavenged reactive oxygen species (damaging molecules). It activated the STAT3 pathway, which helps cell survival. It also blocked amyloid beta from clumping into the toxic oligomers and fibrils that characterize Alzheimer's. HNSS reduced amyloid deposits in neurons and helped immune cells in the brain (microglia) clear amyloid. In 3xTg-AD transgenic mice (a standard Alzheimer's model), HNSS treatment prevented brain neuron loss and improved cognitive performance on memory tests.
Qian, Kang; Yang, Peng; Li, Yixian; Meng, Ran; Cheng, Yunlong; Zhou, Lingling; Wu, Jing; Xu, Shuting; Bao, Xiaoyan; Guo, Qian; Wang, Pengzhen; Xu, Minjun; Sheng, Dongyu; Zhang, Qizhi · Animal Study
Keratin peptides under 3 kDa (KEP1) showed the highest cell-penetrating ability at a concentration of 2 mg/mL. They delivered fluorescein-labeled insulin (FITC-INS) into Caco2 intestinal cells without covalent bonding, meaning the keratin peptides and insulin were simply mixed together. The most effective keratin fragments were 8-19 amino acids long and included hydrophobic peptides (like RVVIEPSPVVV), PPII amphipathic peptides (like PPPVVVTFP), and cysteine-rich peptides (like LCAPTPCGPTPL). Uptake was energy-dependent and primarily used macropinocytosis. The peptides' rich hydrophobic residues and disulfide bonds contributed to their cell-penetrating ability.
Qin, Xiaojie; Guo, Yujie; Li, Ruilin; Bitter, Johannes H; Scott, Elinor L; Zhang, Chunhui · In Vitro
Researchers synthesized oleyl-conjugated peptides of increasing length: oleyl-(WRH)1 through oleyl-(WRH)4. The peptide/siRNA complexes were non-cytotoxic at the working concentration (N/P ratio 40, about 20 μM) against breast cancer (MDA-MB-231, MCF-7), ovarian cancer (SK-OV-3), and normal (HEK-293) cells after 72 hours. Oleyl-(WRH)3 and oleyl-(WRH)4 showed the best siRNA delivery: about 60% and 75% cellular uptake respectively in MDA-MB-231 and SK-OV-3 cells. The complexes formed particles under 200 nm in diameter and remained stable in serum at N/P ratios of 40 or above. Western blot confirmed oleyl-(WRH)4 silenced the STAT3 gene by approximately 75% in MDA-MB-231 breast cancer cells and 45% in SK-OV-3 ovarian cancer cells.
Rai, Mrigank Shekhar; Sajid, Muhammad Imran; Moreno, Jonathan; Parang, Keykavous; Tiwari, Rakesh Kumar · In Vitro
The review compared multiple CPP prediction tools using standard performance metrics (accuracy, sensitivity, specificity, Matthews correlation coefficient) on independent test datasets. Commonly used algorithms include support vector machines (SVM), random forests (RF), gradient-boosted decision trees (GBDT), and various types of artificial neural networks (ANN). The review found that tool performance varies significantly depending on dataset size, feature encoding method, and the specific evaluation metrics used. Key factors that affect prediction accuracy include: the size and quality of the training dataset, how peptide sequences are encoded as numerical features, and whether the tool uses sequence-based, structure-based, or hybrid features. The review emphasizes the importance of evaluating tools on independent test sets rather than cross-validation alone.
Ramasundaram, Maduravani; Sohn, Honglae; Madhavan, Thirumurthy · Review