Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung C-C, O’Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, Cowen-Rivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM (2024) Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630(8016):493–500. https://doi.org/10.1038/s41586-024-07487-w
Article PubMed CAS Google Scholar
Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H (2019) Signalp 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol 37(4):420–423. https://doi.org/10.1038/s41587-019-0036-z
Article PubMed CAS Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Article PubMed CAS Google Scholar
Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, Pereira JH, Rodrigues AV, van Dijk AA, Ebrecht AC, Opperman DJ, Sagmeister T, Buhlheller C, Pavkov-Keller T, Rathinaswamy MK, Dalwadi U, Yip CK, Burke JE, Garcia KC, Grishin NV, Adams PD, Read RJ, Baker D (2021) Accurate prediction of protein structures and interactions using a three-track neural network. Science 373(6557):871–876. https://doi.org/10.1126/science.abj8754
Article PubMed PubMed Central CAS Google Scholar
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (2004) A hidden Markov model method, capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics 5(1):29. https://doi.org/10.1186/1471-2105-5-29
Article PubMed PubMed Central Google Scholar
Bakelar J, Buchanan SK, Noinaj N (2016) The structure of the β-barrel assembly machinery complex. Science 351(6269):180–186. https://doi.org/10.1126/science.aad3460
Article PubMed PubMed Central CAS Google Scholar
Baseer S, Ahmad S, Ranaghan KE, Azam SS (2017) Towards a peptide-based vaccine against Shigella sonnei: a subtractive reverse vaccinology based approach. Biologi: J of the Int Assoc of Biologi Stand 50:87–99. https://doi.org/10.1016/j.biologicals.2017.08.004
Bernhofer M, Rost B (2022) Tmbed: transmembrane proteins predicted through language model embeddings. BMC Bioinform 23(1):326. https://doi.org/10.1186/s12859-022-04873-x
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J (2021) EggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38(12):5825–5829. https://doi.org/10.1093/molbev/msab293
Article PubMed PubMed Central CAS Google Scholar
Casadio R, Martelli PL, Bartoli L, Fariselli P (2010) Topology prediction of membrane proteins: how distantly related homologs come into play. In Struct Bioinform of Membr Prot. https://doi.org/10.1007/978-3-7091-0045-5_4
Castiglione F, Mantile F, De Berardinis P, Prisco A (2012) How the interval between prime and boost injection affects the immune response in a computational model of the immune system. Comput Math Methods Med 2012:842329. https://doi.org/10.1155/2012/842329
Article PubMed PubMed Central CAS Google Scholar
Centers for disease control and prevention (2018). Sexually Transmitted Disease Surveillance. https://doi.org/10.15620/cdc.79370
Cervantes PW, Segelke BW, Lau EY, Robinson BV, Abisoye-Ogunniyan A, Pal S, de la Maza LM, Coleman MA, D’haeseleer P (2024) Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis. PLoS ONE 19(6):e0304525. https://doi.org/10.1371/journal.pone.0304525
Article PubMed PubMed Central CAS Google Scholar
Chen Z, Zhu Y, Sha T, Li Z, Li Y, Zhang F, Ding J (2021) Design of a new multi-epitope vaccine against Brucella based on T and B cell epitopes using bioinformatics methods. Epidemiol Infect 149(e136):e136. https://doi.org/10.1017/S0950268821001229
Article PubMed PubMed Central CAS Google Scholar
Chesson HW, Spicknall IH, Bingham A, Brisson M, Eppink ST, Farnham PG, Kreisel KM, Kumar S, Laprise J-F, Peterman TA, Roberts H, Gift TL (2021) The estimated direct lifetime medical costs of sexually transmitted infections acquired in the United States in 2018. Sex Transm Dis 48(4):215–221. https://doi.org/10.1097/OLQ.0000000000001380
Article PubMed PubMed Central Google Scholar
Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823–826. https://doi.org/10.1002/j.1460-2075.1986.tb04288.x
Article PubMed PubMed Central CAS Google Scholar
de la Maza LM, Zhong G, Brunham RC (2017) Update on chlamydia trachomatis vaccinology. Clinical and Vaccine Immunology: CVI 24(4):e00543-e616. https://doi.org/10.1128/cvi.00543-16
Article PubMed PubMed Central CAS Google Scholar
de la Maza LM, Darville TL, Pal S (2021) Chlamydia trachomatis vaccines for genital infections: where are we and how far is there to go? Expert Rev Vaccines 20(4):421–435. https://doi.org/10.1080/14760584.2021.1899817
Article PubMed PubMed Central CAS Google Scholar
Dimitrov I, Naneva L, Doytchinova I, Bangov I (2014) AllergenFP: allergenicity prediction by descriptor fingerprints. Bioinformatics 30(6):846–851. https://doi.org/10.1093/bioinformatics/btt619
Article PubMed CAS Google Scholar
Dong R, Chu Z, Yu F, Zha Y (2020) Contriving multi-epitope subunit of vaccine for COVID-19: immunoinformatics approaches. Front Immunol 11:1784. https://doi.org/10.3389/fimmu.2020.01784
Article PubMed PubMed Central CAS Google Scholar
Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8(1):4. https://doi.org/10.1186/1471-2105-8-4
Article PubMed PubMed Central CAS Google Scholar
Du Z, Su H, Wang W, Ye L, Wei H, Peng Z, Anishchenko I, Baker D, Yang J (2021) The trRosetta server for fast and accurate protein structure prediction. Nat Protoc 16(12):5634–5651. https://doi.org/10.1038/s41596-021-00628-9
Article PubMed CAS Google Scholar
Elwell C, Mirrashidi K, Engel J (2016) Chlamydia cell biology and pathogenesis. Nat Rev Microbiol 14(6):385–400. https://doi.org/10.1038/nrmicro.2016.30
Article PubMed PubMed Central CAS Google Scholar
Fairman JW, Noinaj N, Buchanan SK (2011) The structural biology of β-barrel membrane proteins: a summary of recent reports. Curr Opin Struct Biol 21(4):523–531. https://doi.org/10.1016/j.sbi.2011.05.005
Article PubMed PubMed Central CAS Google Scholar
Fan H, Zhong G (2015) Chlamydia trachomatis. In Molecular Medical Microbiology. https://doi.org/10.1016/b978-0-12-397169-2.00081-0
Farris CM, Morrison RP (2011) Vaccination against Chlamydia genital infection utilizing the murine C. muridarum model. Infect Immun 79(3):986–996. https://doi.org/10.1128/IAI.00881-10
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