{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:19:12Z","timestamp":1785417552364,"version":"3.56.0"},"reference-count":81,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T00:00:00Z","timestamp":1750636800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T00:00:00Z","timestamp":1750636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Divers"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1007\/s11030-025-11252-0","type":"journal-article","created":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T10:21:53Z","timestamp":1750674113000},"page":"1251-1270","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets"],"prefix":"10.1007","volume":"30","author":[{"given":"Thejaswi","family":"Bhat","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manish","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishna Kumar","family":"Ballamoole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijaya Kumar","family":"Deekshit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavan","family":"Gollapalli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,23]]},"reference":[{"key":"11252_CR1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006258","volume":"14","author":"D Moradigaravand","year":"2018","unstructured":"Moradigaravand D, Palm M, Farewell A et al (2018) Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data. PLoS Comput Biol 14:e1006258. https:\/\/doi.org\/10.1371\/journal.pcbi.1006258","journal-title":"PLoS Comput Biol"},{"key":"11252_CR2","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","volume":"18","author":"E Tacconelli","year":"2018","unstructured":"Tacconelli E, Carrara E, Savoldi A et al (2018) Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis 18:318\u2013327. https:\/\/doi.org\/10.1016\/S1473-3099(17)30753-3","journal-title":"Lancet Infect Dis"},{"key":"11252_CR3","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1128\/CMR.00058-07","volume":"21","author":"AY Peleg","year":"2008","unstructured":"Peleg AY, Seifert H, Paterson DL (2008) Acinetobacter baumannii\u202f: emergence of a successful pathogen. Clin Microbiol Rev 21:538\u2013582. https:\/\/doi.org\/10.1128\/CMR.00058-07","journal-title":"Clin Microbiol Rev"},{"key":"11252_CR4","doi-asserted-by":"publisher","unstructured":"Subhadra B, Hwan Oh M, Hee Choi C, 1 Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea. (2016) Quorum sensing in Acinetobacter: with special emphasis on antibiotic resistance, biofilm formation and quorum quenching. AIMS Microbiol 2:27\u201341. https:\/\/doi.org\/10.3934\/microbiol.2016.1.27","DOI":"10.3934\/microbiol.2016.1.27"},{"key":"11252_CR5","doi-asserted-by":"publisher","first-page":"1127","DOI":"10.1111\/j.1462-5822.2005.00538.x","volume":"7","author":"CH Choi","year":"2005","unstructured":"Choi CH, Lee EY, Lee YC et al (2005) Outer membrane protein 38 of Acinetobacter baumannii localizes to the mitochondria and induces apoptosis of epithelial cells. Cell Microbiol 7:1127\u20131138. https:\/\/doi.org\/10.1111\/j.1462-5822.2005.00538.x","journal-title":"Cell Microbiol"},{"key":"11252_CR6","doi-asserted-by":"publisher","first-page":"373","DOI":"10.3390\/pathogens10030373","volume":"10","author":"I Kyriakidis","year":"2021","unstructured":"Kyriakidis I, Vasileiou E, Pana ZD, Tragiannidis A (2021) Acinetobacter baumannii antibiotic resistance mechanisms. Pathogens 10:373. https:\/\/doi.org\/10.3390\/pathogens10030373","journal-title":"Pathogens"},{"key":"11252_CR7","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2024.106674","volume":"192","author":"S Singh","year":"2024","unstructured":"Singh S, Singh S, Trivedi M, Dwivedi M (2024) An insight into MDR Acinetobacter baumannii infection and its pathogenesis: potential therapeutic targets and challenges. Microb Pathog 192:106674. https:\/\/doi.org\/10.1016\/j.micpath.2024.106674","journal-title":"Microb Pathog"},{"key":"11252_CR8","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1002\/iub.533","volume":"63","author":"GM Cerqueira","year":"2011","unstructured":"Cerqueira GM, Peleg AY (2011) Insights into Acinetobacter baumannii pathogenicity. IUBMB Life 63:1055\u20131060. https:\/\/doi.org\/10.1002\/iub.533","journal-title":"IUBMB Life"},{"key":"11252_CR9","doi-asserted-by":"publisher","first-page":"1332108","DOI":"10.3389\/fmicb.2024.1332108","volume":"15","author":"J Shi","year":"2024","unstructured":"Shi J, Cheng J, Liu S et al (2024) Acinetobacter baumannii: an evolving and cunning opponent. Front Microbiol 15:1332108. https:\/\/doi.org\/10.3389\/fmicb.2024.1332108","journal-title":"Front Microbiol"},{"key":"11252_CR10","doi-asserted-by":"publisher","unstructured":"Lee C-R, Lee JH, Park M et al (2017) Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options. Front Cell Infect Microbiol 7. https:\/\/doi.org\/10.3389\/fcimb.2017.00055","DOI":"10.3389\/fcimb.2017.00055"},{"key":"11252_CR11","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.2165\/11317030-000000000-00000","volume":"69","author":"X-Z Li","year":"2009","unstructured":"Li X-Z, Nikaido H (2009) Efflux-mediated drug resistance in bacteria: an update. Drugs 69:1555\u20131623. https:\/\/doi.org\/10.2165\/11317030-000000000-00000","journal-title":"Drugs"},{"key":"11252_CR12","doi-asserted-by":"publisher","first-page":"197","DOI":"10.3390\/pathogens13030197","volume":"13","author":"KM Zack","year":"2024","unstructured":"Zack KM, Sorenson T, Joshi SG (2024) Types and mechanisms of efflux pump systems and the potential of efflux pump inhibitors in the restoration of antimicrobial susceptibility, with a special reference to Acinetobacter baumannii. Pathogens 13:197. https:\/\/doi.org\/10.3390\/pathogens13030197","journal-title":"Pathogens"},{"key":"11252_CR13","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmgm.2025.108956","volume":"136","author":"S Singh","year":"2025","unstructured":"Singh S, Agarwal J, Das A et al (2025) Leveraging molecular dynamics, physicochemical, and structural analysis to explore OMP33-36 protein as a drug target in Acinetobacter baumannii: an approach against nosocomial infection. J Mol Graph Model 136:108956. https:\/\/doi.org\/10.1016\/j.jmgm.2025.108956","journal-title":"J Mol Graph Model"},{"key":"11252_CR14","doi-asserted-by":"publisher","first-page":"1110125","DOI":"10.3389\/fitd.2023.1110125","volume":"4","author":"N Agyepong","year":"2023","unstructured":"Agyepong N, Fordjour F, Owusu-Ofori A (2023) Multidrug-resistant Acinetobacter baumannii in healthcare settings in Africa. Front Trop Dis 4:1110125. https:\/\/doi.org\/10.3389\/fitd.2023.1110125","journal-title":"Front Trop Dis"},{"key":"11252_CR15","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1186\/s12864-016-2951-4","volume":"17","author":"A Hassan","year":"2016","unstructured":"Hassan A, Naz A, Obaid A et al (2016) Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets. BMC Genomics 17:732. https:\/\/doi.org\/10.1186\/s12864-016-2951-4","journal-title":"BMC Genomics"},{"key":"11252_CR16","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.copbio.2019.12.001","volume":"63","author":"Y Kim","year":"2020","unstructured":"Kim Y, Gu C, Kim HU, Lee SY (2020) Current status of pan-genome analysis for pathogenic bacteria. Curr Opin Biotechnol 63:54\u201362. https:\/\/doi.org\/10.1016\/j.copbio.2019.12.001","journal-title":"Curr Opin Biotechnol"},{"key":"11252_CR17","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.9643","volume":"8","author":"CL Ara\u00fajo","year":"2020","unstructured":"Ara\u00fajo CL, Blanco I, Souza L et al (2020) In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis. PeerJ 8:e9643. https:\/\/doi.org\/10.7717\/peerj.9643","journal-title":"PeerJ"},{"key":"11252_CR18","doi-asserted-by":"publisher","first-page":"D10","DOI":"10.1093\/nar\/gkaa892","volume":"49","author":"EW Sayers","year":"2021","unstructured":"Sayers EW, Beck J, Bolton EE et al (2021) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 49:D10\u2013D17. https:\/\/doi.org\/10.1093\/nar\/gkaa892","journal-title":"Nucleic Acids Res"},{"key":"11252_CR19","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/s13059-019-1841-x","volume":"20","author":"BD Ondov","year":"2019","unstructured":"Ondov BD, Starrett GJ, Sappington A et al (2019) Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biol 20:232. https:\/\/doi.org\/10.1186\/s13059-019-1841-x","journal-title":"Genome Biol"},{"key":"11252_CR20","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","volume":"30","author":"AJ Enright","year":"2002","unstructured":"Enright AJ (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575\u20131584. https:\/\/doi.org\/10.1093\/nar\/30.7.1575","journal-title":"Nucleic Acids Res"},{"key":"11252_CR21","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez-R LM, Phillippy AM et al (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114. https:\/\/doi.org\/10.1038\/s41467-018-07641-9","journal-title":"Nat Commun"},{"key":"11252_CR22","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068\u20132069. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153","journal-title":"Bioinformatics"},{"key":"11252_CR23","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page AJ, Cummins CA, Hunt M et al (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691\u20133693. https:\/\/doi.org\/10.1093\/bioinformatics\/btv421","journal-title":"Bioinformatics"},{"key":"11252_CR24","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1186\/1471-2105-7-409","volume":"7","author":"S Hutter","year":"2006","unstructured":"Hutter S, Vilella AJ, Rozas J (2006) Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinformatics 7:409. https:\/\/doi.org\/10.1186\/1471-2105-7-409","journal-title":"BMC Bioinformatics"},{"key":"11252_CR25","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","volume":"47","author":"J Huerta-Cepas","year":"2019","unstructured":"Huerta-Cepas J, Szklarczyk D, Heller D et al (2019) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47:D309\u2013D314. https:\/\/doi.org\/10.1093\/nar\/gky1085","journal-title":"Nucleic Acids Res"},{"key":"11252_CR26","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I et al (2021) eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38:5825\u20135829. https:\/\/doi.org\/10.1093\/molbev\/msab293","journal-title":"Mol Biol Evol"},{"key":"11252_CR27","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","volume":"11","author":"M Feldgarden","year":"2021","unstructured":"Feldgarden M, Brover V, Gonzalez-Escalona N et al (2021) AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 11:12728. https:\/\/doi.org\/10.1038\/s41598-021-91456-0","journal-title":"Sci Rep"},{"key":"11252_CR28","doi-asserted-by":"publisher","unstructured":"Alcock BP, Raphenya AR, Lau TTY et al (2019) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res: gkz935. https:\/\/doi.org\/10.1093\/nar\/gkz935","DOI":"10.1093\/nar\/gkz935"},{"key":"11252_CR29","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia V, Kaas RS, Ruppe E et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75:3491\u20133500. https:\/\/doi.org\/10.1093\/jac\/dkaa345","journal-title":"J Antimicrob Chemother"},{"key":"11252_CR30","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/AAC.01310-13","volume":"58","author":"SK Gupta","year":"2014","unstructured":"Gupta SK, Padmanabhan BR, Diene SM et al (2014) ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 58:212\u2013220. https:\/\/doi.org\/10.1128\/AAC.01310-13","journal-title":"Antimicrob Agents Chemother"},{"key":"11252_CR31","doi-asserted-by":"publisher","first-page":"D561","DOI":"10.1093\/nar\/gkz1010","volume":"48","author":"E Doster","year":"2020","unstructured":"Doster E, Lakin SM, Dean CJ et al (2020) MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. Nucleic Acids Res 48:D561\u2013D569. https:\/\/doi.org\/10.1093\/nar\/gkz1010","journal-title":"Nucleic Acids Res"},{"key":"11252_CR32","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. https:\/\/doi.org\/10.1186\/1471-2105-10-421","journal-title":"BMC Bioinformatics"},{"key":"11252_CR33","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu Z, Eils R, Schlesner M (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32:2847\u20132849. https:\/\/doi.org\/10.1093\/bioinformatics\/btw313","journal-title":"Bioinformatics"},{"key":"11252_CR34","doi-asserted-by":"publisher","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","volume":"49","author":"D Szklarczyk","year":"2021","unstructured":"Szklarczyk D, Gable AL, Nastou KC et al (2021) The STRING database in 2021: customizable protein\u2013protein networks, and functional characterization of user-uploaded gene\/measurement sets. Nucleic Acids Res 49:D605\u2013D612. https:\/\/doi.org\/10.1093\/nar\/gkaa1074","journal-title":"Nucleic Acids Res"},{"key":"11252_CR35","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/s12859-015-0535-y","volume":"16","author":"T Huo","year":"2015","unstructured":"Huo T, Liu W, Guo Y et al (2015) Prediction of host\u2014pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinformatics 16:100. https:\/\/doi.org\/10.1186\/s12859-015-0535-y","journal-title":"BMC Bioinformatics"},{"key":"11252_CR36","doi-asserted-by":"publisher","first-page":"D374","DOI":"10.1093\/nar\/gkt887","volume":"42","author":"R Mosca","year":"2014","unstructured":"Mosca R, C\u00e9ol A, Stein A et al (2014) 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucl Acids Res 42:D374\u2013D379. https:\/\/doi.org\/10.1093\/nar\/gkt887","journal-title":"Nucl Acids Res"},{"key":"11252_CR37","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1385\/1-59259-890-0:571","volume-title":"The proteomics protocols handbook","author":"E Gasteiger","year":"2005","unstructured":"Gasteiger E, Hoogland C, Gattiker A et al (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana Press, Totowa, NJ, pp 571\u2013607"},{"key":"11252_CR38","doi-asserted-by":"publisher","first-page":"W402","DOI":"10.1093\/nar\/gkz297","volume":"47","author":"DWA Buchan","year":"2019","unstructured":"Buchan DWA, Jones DT (2019) The PSIPRED protein analysis workbench: 20 years on. Nucleic Acids Res 47:W402\u2013W407. https:\/\/doi.org\/10.1093\/nar\/gkz297","journal-title":"Nucleic Acids Res"},{"key":"11252_CR39","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1093\/bioinformatics\/11.6.681","volume":"11","author":"C Geourjon","year":"1995","unstructured":"Geourjon C, Del\u00e9age G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics 11:681\u2013684. https:\/\/doi.org\/10.1093\/bioinformatics\/11.6.681","journal-title":"Bioinformatics"},{"key":"11252_CR40","doi-asserted-by":"publisher","first-page":"W296","DOI":"10.1093\/nar\/gky427","volume":"46","author":"A Waterhouse","year":"2018","unstructured":"Waterhouse A, Bertoni M, Bienert S et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296\u2013W303. https:\/\/doi.org\/10.1093\/nar\/gky427","journal-title":"Nucleic Acids Res"},{"key":"11252_CR41","doi-asserted-by":"publisher","unstructured":"Yang J, Zhang Y (2015) Protein structure and function prediction using I\u2010TASSER. CP Bioinform 52. https:\/\/doi.org\/10.1002\/0471250953.bi0508s52","DOI":"10.1002\/0471250953.bi0508s52"},{"key":"11252_CR42","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbr.2024.100010","volume":"1","author":"PS Sahoo","year":"2024","unstructured":"Sahoo PS, Burra VLSP (2024) Evaluating the 3D structure prediction tools to identify optimal MEBPVC structure models. Comput Struct Biotechnol Rep 1:100010. https:\/\/doi.org\/10.1016\/j.csbr.2024.100010","journal-title":"Comput Struct Biotechnol Rep"},{"key":"11252_CR43","doi-asserted-by":"publisher","first-page":"W384","DOI":"10.1093\/nar\/gkt458","volume":"41","author":"L Heo","year":"2013","unstructured":"Heo L, Park H, Seok C (2013) GalaxyRefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res 41:W384\u2013W388. https:\/\/doi.org\/10.1093\/nar\/gkt458","journal-title":"Nucleic Acids Res"},{"key":"11252_CR44","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283\u2013291. https:\/\/doi.org\/10.1107\/S0021889892009944","journal-title":"J Appl Crystallogr"},{"key":"11252_CR45","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1002\/pro.5560020916","volume":"2","author":"C Colovos","year":"1993","unstructured":"Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511\u20131519. https:\/\/doi.org\/10.1002\/pro.5560020916","journal-title":"Protein Sci"},{"key":"11252_CR46","doi-asserted-by":"publisher","first-page":"W407","DOI":"10.1093\/nar\/gkm290","volume":"35","author":"M Wiederstein","year":"2007","unstructured":"Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407\u2013W410. https:\/\/doi.org\/10.1093\/nar\/gkm290","journal-title":"Nucleic Acids Res"},{"key":"11252_CR47","doi-asserted-by":"publisher","first-page":"2041","DOI":"10.1021\/ci100241y","volume":"50","author":"A Volkamer","year":"2010","unstructured":"Volkamer A, Griewel A, Grombacher T, Rarey M (2010) Analyzing the topology of active sites: on the prediction of pockets and subpockets. J Chem Inf Model 50:2041\u20132052. https:\/\/doi.org\/10.1021\/ci100241y","journal-title":"J Chem Inf Model"},{"key":"11252_CR48","doi-asserted-by":"publisher","first-page":"W363","DOI":"10.1093\/nar\/gky473","volume":"46","author":"W Tian","year":"2018","unstructured":"Tian W, Chen C, Lei X et al (2018) CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res 46:W363\u2013W367. https:\/\/doi.org\/10.1093\/nar\/gky473","journal-title":"Nucleic Acids Res"},{"key":"11252_CR49","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1021\/ci5006004","volume":"55","author":"A Borrel","year":"2015","unstructured":"Borrel A, Regad L, Xhaard H et al (2015) PockDrug: a model for predicting pocket druggability that overcomes pocket estimation uncertainties. J Chem Inf Model 55:882\u2013895. https:\/\/doi.org\/10.1021\/ci5006004","journal-title":"J Chem Inf Model"},{"key":"11252_CR50","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1002\/jcb.29953","volume":"123","author":"S Basu","year":"2022","unstructured":"Basu S, Naha A, Veeraraghavan B et al (2022) In silico structure evaluation of BAG3 and elucidating its association with bacterial infections through protein\u2013protein and host-pathogen interaction analysis. J of Cellular Biochem 123:115\u2013127. https:\/\/doi.org\/10.1002\/jcb.29953","journal-title":"J of Cellular Biochem"},{"key":"11252_CR51","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1101\/gr.849004","volume":"14","author":"GE Crooks","year":"2004","unstructured":"Crooks GE, Hon G, Chandonia J-M, Brenner SE (2004) WebLogo: a sequence logo generator: figure 1. Genome Res 14:1188\u20131190. https:\/\/doi.org\/10.1101\/gr.849004","journal-title":"Genome Res"},{"key":"11252_CR52","doi-asserted-by":"publisher","first-page":"W39","DOI":"10.1093\/nar\/gkv416","volume":"43","author":"TL Bailey","year":"2015","unstructured":"Bailey TL, Johnson J, Grant CE, Noble WS (2015) The MEME suite. Nucleic Acids Res 43:W39\u2013W49. https:\/\/doi.org\/10.1093\/nar\/gkv416","journal-title":"Nucleic Acids Res"},{"key":"11252_CR53","doi-asserted-by":"publisher","first-page":"39454","DOI":"10.1021\/acsomega.3c05210","volume":"8","author":"SCM Peela","year":"2023","unstructured":"Peela SCM, Basu S, Sharma J et al (2023) Structure elucidation and interaction dynamics of MefA-MsrD efflux proteins in Streptococcus pneumoniae: impact on macrolide susceptibility. ACS Omega 8:39454\u201339467. https:\/\/doi.org\/10.1021\/acsomega.3c05210","journal-title":"ACS Omega"},{"key":"11252_CR54","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2022.e11232","volume":"8","author":"SK Paul","year":"2022","unstructured":"Paul SK, Saddam Md, Rahaman KA et al (2022) Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: an upregulated biomarker in experimental autoimmune encephalomyelitis mice. Heliyon 8:e11232. https:\/\/doi.org\/10.1016\/j.heliyon.2022.e11232","journal-title":"Heliyon"},{"key":"11252_CR55","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1529\/biophysj.107.120501","volume":"95","author":"S Haider","year":"2008","unstructured":"Haider S, Parkinson GN, Neidle S (2008) Molecular dynamics and principal components analysis of human telomeric quadruplex multimers. Biophys J 95:296\u2013311. https:\/\/doi.org\/10.1529\/biophysj.107.120501","journal-title":"Biophys J"},{"key":"11252_CR56","unstructured":"Souza CR de (2012) A tutorial on principal component analysis with the accord. NET Framework"},{"key":"11252_CR57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1046\/j.1462-2920.2001.00161.x","volume":"3","author":"A Alonso","year":"2001","unstructured":"Alonso A, S\u00e1nchez P, Mart\u00ednez JL (2001) Environmental selection of antibiotic resistance genes: minireview. Environ Microbiol 3:1\u20139. https:\/\/doi.org\/10.1046\/j.1462-2920.2001.00161.x","journal-title":"Environ Microbiol"},{"key":"11252_CR58","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/nrmicro2312","volume":"8","author":"HK Allen","year":"2010","unstructured":"Allen HK, Donato J, Wang HH et al (2010) Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 8:251\u2013259. https:\/\/doi.org\/10.1038\/nrmicro2312","journal-title":"Nat Rev Microbiol"},{"key":"11252_CR59","doi-asserted-by":"publisher","first-page":"D767","DOI":"10.1093\/nar\/gkac832","volume":"51","author":"Y Zhang","year":"2023","unstructured":"Zhang Y, Zhang H, Zhang Z et al (2023) ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics. Nucleic Acids Res 51:D767\u2013D776. https:\/\/doi.org\/10.1093\/nar\/gkac832","journal-title":"Nucleic Acids Res"},{"key":"11252_CR60","doi-asserted-by":"publisher","unstructured":"Gollapalli P et al (2021) Network topology analysis of essential genes interactome of Helicobacter pylori to explore novel therapeutic targets. Microbial Pathogenesis 158:105059. https:\/\/doi.org\/10.1016\/j.micpath.2021.105059","DOI":"10.1016\/j.micpath.2021.105059"},{"key":"11252_CR61","doi-asserted-by":"publisher","first-page":"53","DOI":"10.5808\/GI.2015.13.2.53","volume":"13","author":"MdS Islam","year":"2015","unstructured":"Islam MdS, Shahik SMd, Sohel Md et al (2015) In Silico structural and functional annotation of hypothetical proteins of Vibrio cholerae O139. Genomics Inform 13:53. https:\/\/doi.org\/10.5808\/GI.2015.13.2.53","journal-title":"Genomics Inform"},{"key":"11252_CR62","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1093\/protein\/4.2.155","volume":"4","author":"K Guruprasad","year":"1990","unstructured":"Guruprasad K, Reddy BVB, Pandit MW (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng Des Sel 4:155\u2013161. https:\/\/doi.org\/10.1093\/protein\/4.2.155","journal-title":"Protein Eng Des Sel"},{"key":"11252_CR63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0198965","volume":"13","author":"WLO Da Costa","year":"2018","unstructured":"Da Costa WLO, Ara\u00fajo CLDA, Dias LM et al (2018) Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PLoS ONE 13:e0198965. https:\/\/doi.org\/10.1371\/journal.pone.0198965","journal-title":"PLoS ONE"},{"key":"11252_CR64","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1006\/jmbi.1996.0628","volume":"264","author":"J Pontius","year":"1996","unstructured":"Pontius J, Richelle J, Wodak SJ (1996) Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 264:121\u2013136. https:\/\/doi.org\/10.1006\/jmbi.1996.0628","journal-title":"J Mol Biol"},{"key":"11252_CR65","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/s12866-021-02107-3","volume":"21","author":"T Gao","year":"2021","unstructured":"Gao T, Gao Y, Liu X et al (2021) Identification and functional analysis of the SARS-COV-2 nucleocapsid protein. BMC Microbiol 21:58. https:\/\/doi.org\/10.1186\/s12866-021-02107-3","journal-title":"BMC Microbiol"},{"key":"11252_CR66","doi-asserted-by":"publisher","first-page":"2150","DOI":"10.1093\/bioinformatics\/btu184","volume":"30","author":"M Jamroz","year":"2014","unstructured":"Jamroz M, Kolinski A, Kmiecik S (2014) CABS-flex predictions of protein flexibility compared with NMR ensembles. Bioinformatics 30:2150\u20132154. https:\/\/doi.org\/10.1093\/bioinformatics\/btu184","journal-title":"Bioinformatics"},{"key":"11252_CR67","doi-asserted-by":"publisher","DOI":"10.1016\/j.crstbi.2024.100127","volume":"7","author":"SK Bhati","year":"2024","unstructured":"Bhati SK, Jain M, Muthukumaran J, Singh AK (2024) Computational identification of candidate inhibitors for Dihydrofolate reductase in Acinetobacter baumannii. Curr Res Struct Biol 7:100127. https:\/\/doi.org\/10.1016\/j.crstbi.2024.100127","journal-title":"Curr Res Struct Biol"},{"key":"11252_CR68","doi-asserted-by":"publisher","first-page":"34984","DOI":"10.1038\/srep34984","volume":"6","author":"I Aier","year":"2016","unstructured":"Aier I, Varadwaj PK, Raj U (2016) Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Sci Rep 6:34984. https:\/\/doi.org\/10.1038\/srep34984","journal-title":"Sci Rep"},{"key":"11252_CR69","doi-asserted-by":"publisher","first-page":"1950","DOI":"10.1002\/prot.22711","volume":"78","author":"K Lindorff-Larsen","year":"2010","unstructured":"Lindorff-Larsen K, Piana S, Palmo K et al (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78:1950\u20131958. https:\/\/doi.org\/10.1002\/prot.22711","journal-title":"Proteins"},{"key":"11252_CR70","doi-asserted-by":"publisher","first-page":"43807","DOI":"10.1038\/srep43807","volume":"7","author":"MA Anwar","year":"2017","unstructured":"Anwar MA, Choi S (2017) Structure-activity relationship in TLR4 mutations: atomistic molecular dynamics simulations and residue interaction network analysis. Sci Rep 7:43807. https:\/\/doi.org\/10.1038\/srep43807","journal-title":"Sci Rep"},{"key":"11252_CR71","doi-asserted-by":"publisher","first-page":"1601","DOI":"10.3389\/fmicb.2019.01601","volume":"10","author":"FC Morris","year":"2019","unstructured":"Morris FC, Dexter C, Kostoulias X et al (2019) The mechanisms of disease caused by Acinetobacter baumannii. Front Microbiol 10:1601. https:\/\/doi.org\/10.3389\/fmicb.2019.01601","journal-title":"Front Microbiol"},{"key":"11252_CR72","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1016\/j.synbio.2022.04.011","volume":"7","author":"OS Mohite","year":"2022","unstructured":"Mohite OS, Lloyd CJ, Monk JM et al (2022) Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets. Synth Syst Biotechnol 7:900\u2013910. https:\/\/doi.org\/10.1016\/j.synbio.2022.04.011","journal-title":"Synth Syst Biotechnol"},{"key":"11252_CR73","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.mib.2014.11.016","volume":"23","author":"G Vernikos","year":"2015","unstructured":"Vernikos G, Medini D, Riley DR, Tettelin H (2015) Ten years of pan-genome analyses. Curr Opin Microbiol 23:148\u2013154. https:\/\/doi.org\/10.1016\/j.mib.2014.11.016","journal-title":"Curr Opin Microbiol"},{"key":"11252_CR74","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.gene.2017.04.019","volume":"623","author":"T Bhardwaj","year":"2017","unstructured":"Bhardwaj T, Somvanshi P (2017) Pan-genome analysis of Clostridium botulinum reveals unique targets for drug development. Gene 623:48\u201362. https:\/\/doi.org\/10.1016\/j.gene.2017.04.019","journal-title":"Gene"},{"key":"11252_CR75","doi-asserted-by":"publisher","first-page":"119","DOI":"10.3390\/antibiotics9030119","volume":"9","author":"C Ayoub Moubareck","year":"2020","unstructured":"Ayoub Moubareck C, Hammoudi Halat D (2020) Insights into Acinetobacter baumannii: a review of microbiological, virulence, and resistance traits in a threatening nosocomial pathogen. Antibiotics 9:119. https:\/\/doi.org\/10.3390\/antibiotics9030119","journal-title":"Antibiotics"},{"key":"11252_CR76","doi-asserted-by":"publisher","unstructured":"Singh S, Agarwal J, Das A et al (2025) An evolutionary attributes of OMP33-36 in Acinetobacter baumannii: in silico based analysis. CP 22. https:\/\/doi.org\/10.2174\/0115701646354315241231094038","DOI":"10.2174\/0115701646354315241231094038"},{"key":"11252_CR77","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2023.105549","volume":"118","author":"N Verma","year":"2024","unstructured":"Verma N, Sharma T, Bhardwaj A, Vemuluri VR (2024) Comparative genomics and characterization of a multidrug-resistant Acinetobacter baumannii VRL-M19 isolated from a crowded setting in India. Infect Genet Evol 118:105549. https:\/\/doi.org\/10.1016\/j.meegid.2023.105549","journal-title":"Infect Genet Evol"},{"key":"11252_CR78","doi-asserted-by":"publisher","first-page":"2407","DOI":"10.1021\/ar300327a","volume":"46","author":"DA Leonard","year":"2013","unstructured":"Leonard DA, Bonomo RA, Powers RA (2013) Class D \u03b2-lactamases: a reappraisal after five decades. Acc Chem Res 46:2407\u20132415. https:\/\/doi.org\/10.1021\/ar300327a","journal-title":"Acc Chem Res"},{"key":"11252_CR79","doi-asserted-by":"publisher","unstructured":"Vasconcelos ALS, Andreote FD, Defalco T et al (2022) Mucilaginibacter sp. Strain metal(loid) and antibiotic resistance isolated from estuarine soil contaminated mine tailing from the Fund\u00e3o Dam. Genes 13:174. https:\/\/doi.org\/10.3390\/genes13020174","DOI":"10.3390\/genes13020174"},{"key":"11252_CR80","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/S1570-0232(02)00054-5","volume":"771","author":"S Sinchaikul","year":"2002","unstructured":"Sinchaikul S, Sookkheo B, Topanuruk S et al (2002) Bioinformatics, functional genomics, and proteomics study of Bacillus sp. J Chromatogr B 771:261\u2013287. https:\/\/doi.org\/10.1016\/S1570-0232(02)00054-5","journal-title":"J Chromatogr B"},{"key":"11252_CR81","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1016\/S0969-2126(00)00534-7","volume":"8","author":"L Maveyraud","year":"2000","unstructured":"Maveyraud L, Golemi D, Kotra LP et al (2000) Insights into class D \u03b2-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa. Structure 8:1289\u20131298. https:\/\/doi.org\/10.1016\/S0969-2126(00)00534-7","journal-title":"Structure"}],"container-title":["Molecular Diversity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-025-11252-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11030-025-11252-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-025-11252-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,22]],"date-time":"2026-02-22T15:57:10Z","timestamp":1771775830000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11030-025-11252-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,23]]},"references-count":81,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["11252"],"URL":"https:\/\/doi.org\/10.1007\/s11030-025-11252-0","relation":{},"ISSN":["1381-1991","1573-501X"],"issn-type":[{"value":"1381-1991","type":"print"},{"value":"1573-501X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,23]]},"assertion":[{"value":"20 January 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 May 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 June 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"NA.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics statement"}}]}}