Wp SE, Norhidayah M, Ar MNA (2025) Factors associated with multidrug-resistant organism (MDRO) mortality: an analysis from the national surveillance of multidrug-resistant organism, 2018-2022. BMC Infect Dis 25:60. https://doi.org/10.1186/s12879-024-10338-8

Article  PubMed  PubMed Central  CAS  Google Scholar 

Varela MF, Stephen J, Lekshmi M et al (2021) Bacterial resistance to antimicrobial agents. Antibiot Basel Switz 10:593. https://doi.org/10.3390/antibiotics10050593

Article  CAS  Google Scholar 

Dai C, Liu Y, Lv F et al (2025) An alternative approach to combat multidrug-resistant bacteria: new insights into traditional Chinese medicine monomers combined with antibiotics. Adv Biotechnol 3:6. https://doi.org/10.1007/s44307-025-00059-7

Article  CAS  Google Scholar 

Grigson SR, McKerral JC, Mitchell JG et al (2022) Organizing the bacterial annotation space with amino acid sequence embeddings. BMC Bioinform 23:385. https://doi.org/10.1186/s12859-022-04930-5

Article  CAS  Google Scholar 

Mozaffari S, Moen A, Ng CY et al (2025) Structural bioinformatics for rational drug design. Res Pract Thromb Haemost 9:102691. https://doi.org/10.1016/j.rpth.2025.102691

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ouma RBO, Ngari SM, Kibet JK (2024) A review of the current trends in computational approaches in drug design and metabolism. Discov Public Health 21:108. https://doi.org/10.1186/s12982-024-00229-3

Article  Google Scholar 

Pitarch B, Pazos F (2025) Deep learning approaches for the prediction of protein functional sites. Molecules 30:214. https://doi.org/10.3390/molecules30020214

Article  PubMed  PubMed Central  CAS  Google Scholar 

Mao Y, Xu W, Shun Y et al (2025) A multimodal model for protein function prediction. Sci Rep 15:10465. https://doi.org/10.1038/s41598-025-94612-y

Article  PubMed  PubMed Central  CAS  Google Scholar 

Wang J, Watson JL, Lisanza SL (2024) Protein design using structure-prediction networks: AlphaFold and RoseTTAFold as protein structure foundation models. Cold Spring Harb Perspect Biol 16:a041472. https://doi.org/10.1101/cshperspect.a041472

Article  PubMed  PubMed Central  CAS  Google Scholar 

Surur AK, de Oliveira AB, De Annunzio SR et al (2024) Bacterial resistance to antimicrobial photodynamic therapy: a critical update. J Photochem Photobiol B 255:112905. https://doi.org/10.1016/j.jphotobiol.2024.112905

Article  PubMed  CAS  Google Scholar 

Varela MF, Kumar S (2019) Strategies for discovery of new molecular targets for anti-infective drugs. Curr Opin Pharmacol 48:57–68. https://doi.org/10.1016/j.coph.2019.04.015

Article  PubMed  CAS  Google Scholar 

Ren Y, Chakraborty T, Doijad S et al (2022) Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Bioinformatics 38:325–334. https://doi.org/10.1093/bioinformatics/btab681

Article  PubMed  PubMed Central  CAS  Google Scholar 

Clarke D, Bhardwaj N, Gerstein MB (2012) Novel insights through the integration of structural and functional genomics data with protein networks. J Struct Biol 179:320–326. https://doi.org/10.1016/j.jsb.2012.02.001

Article  PubMed  PubMed Central  CAS  Google Scholar 

Munir A, Vedithi SC, Chaplin AK et al (2020) Genomics, computational biology and drug discovery for mycobacterial infections: fighting the emergence of resistance. Front Genet 11:965. https://doi.org/10.3389/fgene.2020.00965

Article  PubMed  PubMed Central  CAS  Google Scholar 

Nagarajan D, Nagarajan T, Roy N et al (2018) Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria. J Biol Chem 293:3492–3509. https://doi.org/10.1074/jbc.M117.805499

Article  PubMed  CAS  Google Scholar 

Priyamvada P, Debroy R, Anbarasu A et al (2022) A comprehensive review on genomics, systems biology and structural biology approaches for combating antimicrobial resistance in ESKAPE pathogens: computational tools and recent advancements. World J Microbiol Biotechnol 38:153. https://doi.org/10.1007/s11274-022-03343-z

Article  PubMed  CAS  Google Scholar 

Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589. https://doi.org/10.1038/s41586-021-03819-2

Article  PubMed  PubMed Central  CAS  Google Scholar 

Varadi M, Bertoni D, Magana P et al (2024) AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res 52:D368–D375. https://doi.org/10.1093/nar/gkad1011

Article  PubMed  PubMed Central  CAS  Google Scholar 

Baek M, DiMaio F, Anishchenko I et al (2021) Accurate prediction of protein structures and interactions using a three-track neural network. Science 373:871–876. https://doi.org/10.1126/science.abj8754

Article  PubMed  PubMed Central  CAS  Google Scholar 

Li H, Lei Y, Zeng J (2024) Revolutionizing biomolecular structure determination with artificial intelligence. Natl Sci Rev 11:nwae339. https://doi.org/10.1093/nsr/nwae339

Article  PubMed  PubMed Central  CAS  Google Scholar 

Guo H-B, Perminov A, Bekele S et al (2022) AlphaFold2 models indicate that protein sequence determines both structure and dynamics. Sci Rep 12:10696. https://doi.org/10.1038/s41598-022-14382-9

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kryshtafovych A, Schwede T, Topf M et al (2021) Critical assessment of methods of protein structure prediction (CASP)—round XIV. Proteins Struct Funct Bioinform 89:1607–1617. https://doi.org/10.1002/prot.26237

Article  CAS  Google Scholar 

Senior AW, Evans R, Jumper J et al (2020) Improved protein structure prediction using potentials from deep learning. Nature 577:706–710. https://doi.org/10.1038/s41586-019-1923-7

Article  PubMed  CAS  Google Scholar 

David A, Islam S, Tankhilevich E, Sternberg MJE (2022) The AlphaFold database of protein structures: a biologist’s guide. J Mol Biol 434:167336. https://doi.org/10.1016/j.jmb.2021.167336

Article  PubMed  CAS  Google Scholar 

Price MN, Wetmore KM, Waters RJ et al (2018) Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 557:503–509. https://doi.org/10.1038/s41586-018-0124-0

Article  PubMed  CAS  Google Scholar 

Price MN, Arkin AP (2024) Interactive tools for functional annotation of bacterial genomes. Database 2024:baae089. https://doi.org/10.1093/database/baae089

Article  PubMed  PubMed Central  CAS  Google Scholar 

Powers R, Copeland JC, Germer K et al (2006) Comparison of protein active site structures for functional annotation of proteins and drug design. Proteins Struct Funct Bioinform 65:124–135. https://doi.org/10.1002/prot.21092

Article  CAS  Google Scholar 

Redfern O, Bennett C, Orengo C (2005) Structure comparison and protein structure classifications. In: Encyclopedia of genetics, genomics, proteomics and bioinformatics. John Wiley & Sons, Ltd

Massova I, Mobashery S (1998) Kinship and diversification of bacterial penicillin-binding proteins and β-lactamases. Antimicrob Agents Chemother 42:1–17.