Page 112 - MI-2-4
P. 112

Microbes & Immunity                                         Brachyspira pilosicoli novel outer membrane proteins



               beta-barrel outer membrane proteins.  Front Bioinform.   52.  Holm L. Using dali for protein structure comparison.
               2021;1:646581.                                     Methods Mol Biol. 2020;2112:29-42.
               doi: 10.3389/fbinf.2021.646581                     doi: 10.1007/978-1-0716-0270-6_3
            40.  Bagos PG, LiakopoulipopTD, Hamodrakas SJ. Finding beta-  53.  Van Kempen M, Kim SS, Tumescheit C,  et al. Fast and
               barrel outer membrane proteins with a markov chain model.   accurate protein structure search with foldseek.  Nat
               WSEAS Trans Biol Biomed. 2004;2(1):186-189.        Biotechnol. 2024;42(2):243-246.
            41.  Ou YY, Gromiha MM, Chen SA, Suwa M. TMBETADISC-     doi: 10.1038/s41587-023-01773-0
               RBF:  Discrimination  of  beta-barrel  membrane  proteins
               using RBF networks and PSSM profiles. Comput Biol Chem.   54.  Törönen P, Holm L. PANNZER-a practical tool for protein
                                                                  function prediction. Protein Sci. 2022;31(1):118-128.
               2008;32(3):227-231.
                                                                  doi: 10.1002/pro.4193
               doi: 10.1016/j.compbiolchem.2008.03.002
                                                               55.  Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork  P,
            42.  Bernhofer M, Rost B. TMbed: Transmembrane proteins
               predicted through language model embeddings.  BMC   Huerta-Cepas J. EggNOG-mapper v2: Functional annotation,
               Bioinformatics. 2022;23(1):326.                    orthology assignments, and domain prediction at the
                                                                  metagenomic scale. Mol Biol Evol. 2021;38(12):5825-5829.
               doi: 10.1186/s12859-022-04873-x
                                                                  doi: 10.1093/molbev/msab293
            43.  Abramson J, Adler J, Dunger J,  et al. Accurate structure
               prediction of biomolecular interactions with AlphaFold 3.   56.  Larkin MA, Blackshields G, Brown NP, et al. Clustal W and
               Nature. 2024;630:493-500.                          clustal X version 2.0. Bioinformatics. 2007;23(21):2947-2948.
               doi: 10.1038/s41586-024-07487-w                    doi: 10.1093/bioinformatics/btm404
            44.  Xu J, Zhang Y. How significant is a protein structure similarity   57.  Kumar S, Stecher G, Suleski M, Sanderford M, Sharma S,
               with TM-score= 0.5? Bioinformatics. 2010;26(7):889-895.  Tamura  K.  MEGA12:  Molecular  evolutionary  genetic
                                                                  analysis version 12 for adaptive and green computing. Mol
               doi: 10.1093/bioinformatics/btq066                 Biol Evol. 2024;41(12):msae263.
            45.  Zhang Y, Skolnick J. Scoring function for automated      doi: 10.1093/molbev/msae263
               assessment of protein structure template quality.  Proteins.
               2004;57(4):702-710.                             58.  Zhang C, Shine M, Pyle AM, Zhang Y. US-align: Universal
                                                                  structure alignments of proteins, nucleic acids, and
               doi: 10.1002/prot.20264                            macromolecular complexes. Nat Methods. 2022;19(9):1109-1115.
            46.  DeLano WL. The PyMOL Molecular Graphics System; 2002.      doi: 10.1038/s41592-022-01585-1
               https://www/pymol/org [Last accessed on 2025 Jan 25].
                                                               59.  Derbyshire MC. Bioinformatic detection of positive
            47.  Lin Z, Akin H, Rao R, et al. Evolutionary-scale prediction   selection pressure in plant pathogens: The neutral theory
               of atomic-level protein structure with a language model.   of molecular sequence evolution in action. Front Microbiol.
               Science. 2023;379(6637):1123-1130.                 2020;11:644.
               doi: 10.1126/science.ade2574                       doi: 10.3389/fmicb.2020.00644
            48.  Waterhouse A, Bertoni M, Bienert S, et al. SWISS-MODEL:   60.  Bakelar J, Buchanan SK, Noinaj N. The structure of
               Homology modelling of protein structures and complexes.   the  β-barrel assembly machinery complex.  Science.
               Nucleic Acids Res. 2018;46(W1):W296-W303.          2016;351(6269):180-186.
               doi: 10.1093/nar/gky427                            doi: 10.1126/science.aad3460
            49.  Baek M, DiMaio F, Anishchenko I, et al. Accurate prediction   61.  Konovalova A, Kahne DE, Silhavy TJ. Outer membrane
               of protein structures and interactions using a three-track   biogenesis. Annu Rev Microbiol. 2017;71(1):539-556.
               neural network. Science. 2021;373(6557):871-876.
                                                                  doi: 10.1146/annurev-micro-090816-093754
               doi: 10.1126/science.abj8754
                                                               62.  Lysnyansky I, Ron Y, Sachse K, Yogev D. Intrachromosomal
            50.  Du Z, Su H, Wang W, et al. The trRosetta server for fast   recombination within  the  vsp  locus  of  Mycoplasma bovis
               and accurate protein structure  prediction.  Nat Protoc.   generates a chimeric variable surface lipoprotein antigen.
               2021;16(12):5634-5651.                             Infect Immun. 2001;69(6):3703-3712.
               doi: 10.1038/s41596-021-00628-9                    doi: 10.1128/iai.69.6.3703-3712.2001
            51.  Holm L. Dali server: Structural unification of protein   63.  Gabe JD, Dragon E, Chang RJ, McCaman MT. Identification
               families. Nucleic Acids Res. 2022;50(W1):W210-W215.
                                                                  of a linked set of genes in Serpulina hyodysenteriae
               doi: 10.1093/nar/gkac387                           (B204)  predicted  to encode closely related 39-kilodalton


            Volume 2 Issue 4 (2025)                        104                           doi: 10.36922/MI025230050
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