{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T00:08:38Z","timestamp":1783037318303,"version":"3.54.6"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2012,10,25]],"date-time":"2012-10-25T00:00:00Z","timestamp":1351123200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2013,3]]},"DOI":"10.1007\/s00894-012-1635-5","type":"journal-article","created":{"date-parts":[[2012,10,24]],"date-time":"2012-10-24T08:24:49Z","timestamp":1351067089000},"page":"973-983","source":"Crossref","is-referenced-by-count":14,"title":["Interaction of dihydrofolate reductase and aminoglycoside adenyltransferase enzyme from Klebsiella pneumoniae multidrug resistant strain DF12SA with clindamycin: a molecular modelling and docking study"],"prefix":"10.1007","volume":"19","author":[{"given":"Shailesh K.","family":"Shahi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinay K.","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashok","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjeev K.","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surya K.","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2012,10,25]]},"reference":[{"key":"1635_CR1","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.2337\/dc06-0116","volume":"29","author":"R Gadepalli","year":"2006","unstructured":"Gadepalli R, Dhawan B, Sreenivas V, Kapil A, Ammini AC, Chaudhry R (2006) A clinico-microbiological study of diabetic foot ulcers in an Indian tertiary care hospital. Diabetes Care 29:1727\u20131732","journal-title":"Diabetes Care"},{"key":"1635_CR2","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1177\/107110070502600112","volume":"26","author":"MS Pinzur","year":"2005","unstructured":"Pinzur MS, Slovenkai MP, Trepman E, Shields NN (2005) Guidelines for diabetic foot care: recommendations endorsed by the diabetes committee of the American orthopaedic foot and ankle society. Foot Ankle Int 26:113\u2013119","journal-title":"Foot Ankle Int"},{"key":"1635_CR3","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1086\/424846","volume":"39","author":"BA Lipsky","year":"2004","unstructured":"Lipsky BA, Berendt AR, Deery HG, Embi JM, Joseph WS, Karchmer AW, LeFrock JL, Lew DP, Mader JT, Norden C, Tan JS (2004) Diagnosis and treatment of diabetic foot infections. Clin Infect Diseases 39:885\u2013910","journal-title":"Clin Infect Diseases"},{"key":"1635_CR4","first-page":"15","volume":"45","author":"DA Chincholikar","year":"2002","unstructured":"Chincholikar DA, Pal RB (2002) Study of fungal and bacterial infections of the diabetic foot. Indian J Pathol Microbiol 45:15\u201322","journal-title":"Indian J Pathol Microbiol"},{"key":"1635_CR5","doi-asserted-by":"crossref","first-page":"12","DOI":"10.7713\/ijms.2011.0004","volume":"2","author":"S Umadevi","year":"2011","unstructured":"Umadevi S, Kumar S, Joseph NM, Easow JM, Kandhakumari G, Srirangaraj S, Raj S, Stephen S (2011) Microbiological study of diabetic foot infections. Indian J Med Specialit 2:12\u201317","journal-title":"Indian J Med Specialit"},{"key":"1635_CR6","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1086\/503429","volume":"42","author":"T Kawai","year":"2006","unstructured":"Kawai T (2006) Hypermucoviscosity: an extremely sticky phenotype of Klebsiella pneumoniae associated with emerging destructive tissue abscess syndrome. Clin Infect Dis 42:1359\u20131361","journal-title":"Clin Infect Dis"},{"key":"1635_CR7","doi-asserted-by":"crossref","first-page":"1742","DOI":"10.1016\/S0140-6736(05)62954-6","volume":"349","author":"ME Jones","year":"1997","unstructured":"Jones ME, Peters E, Weersink AM, Fluit A, Verhoef J (1997) Widespread occurrence of integrons causing multiple antibiotic resistances in bacteria. Lancet 349:1742\u20131743","journal-title":"Lancet"},{"key":"1635_CR8","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1111\/j.1472-765X.2010.02926.x","volume":"51","author":"NG El-Najjar","year":"2010","unstructured":"El-Najjar NG, Farah MJ, Hashwa FA, Tokajian ST (2010) Antibiotic resistance patterns and sequencing of class I integron from uropathogenic Escherichia coli in Lebanon. Lett Appl Microbiol 51:456\u2013461","journal-title":"Lett Appl Microbiol"},{"key":"1635_CR9","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/nrmicro1462","volume":"4","author":"D Mazel","year":"2006","unstructured":"Mazel D (2006) Integrons: agents of bacterial evolution. Nat Rev Microbiol 4:608\u2013620","journal-title":"Nat Rev Microbiol"},{"key":"1635_CR10","doi-asserted-by":"crossref","first-page":"2813","DOI":"10.1128\/JCM.40.8.2813-2822.2002","volume":"40","author":"WA Gebreyes","year":"2002","unstructured":"Gebreyes WA, Altier C (2002) Molecular characterization of multidrug-resistant Salmonella enterica subsp. enterica serovar Typhimurium isolates from swine. J Clin Microbiol 40:2813\u20132822","journal-title":"J Clin Microbiol"},{"key":"1635_CR11","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.ajhg.2011.01.007","volume":"88","author":"C Holger","year":"2011","unstructured":"Holger C, Smith DEC, Blom H, Blau N, Bode H, Holzmann K, Pannicke U, Hopfner KP, Rump EM, Ayric Z, Kohne E, Debatin KM, Smulders Y, Schwarz K (2011) Dihydrofolate reductase deficiency due to a homozygous DHFR mutation causes megaloblastic anemia and cerebral folate deficiency leading to severe neurologic disease. Am Soc Human Genet 88:226\u2013231","journal-title":"Am Soc Human Genet"},{"key":"1635_CR12","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1146\/annurev.biophys.33.110502.133613","volume":"33","author":"JR Schnell","year":"2004","unstructured":"Schnell JR, Dyson HJ, Wright PE (2004) Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu Rev Biophys Biomol Struct 33:119\u2013140","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"1635_CR13","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1006\/jmbi.2000.3570","volume":"297","author":"D Thomas","year":"2000","unstructured":"Thomas D, Guenter A, Gerd B, Uwe J, Tarmo P, Robert H, Rainer J (2000) The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability. J Mol Biol 297:659\u2013672","journal-title":"J Mol Biol"},{"key":"1635_CR14","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1021\/ja964278w","volume":"119","author":"E Azucena","year":"1997","unstructured":"Azucena E, Grapsas I, Mobashery S (1997) Properties of a bifunctional bacterial antibiotic resistance enzyme that catalyzes ATP dependent 2\u2033-phosphorylation and acetyl-CoA dependent 6\u2032-acetylation of aminoglycosides. J Am Chem Soc 119:2317\u20132318","journal-title":"J Am Chem Soc"},{"key":"1635_CR15","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1128\/jb.167.2.631-638.1986","volume":"167","author":"JJ Ferretti","year":"1986","unstructured":"Ferretti JJ, Gilmore KS, Courvallin P (1986) Nucleotide sequence analysis of the gene specifying the bifunctional 6\u2032-aminoglycoside acetyltransferase 2\u2033-aminoglycoside phosphotransferase enzyme in Streptococcus faecalis and identification and cloning of gene regions specifying the two activities. J Bacteriol 167:631\u2013638","journal-title":"J Bacteriol"},{"key":"1635_CR16","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1177\/107110078100200202","volume":"2","author":"FW Wagner","year":"1981","unstructured":"Wagner FW (1981) The dysvascular foot: a system for diagnosis and treatment. Foot Ankle 2:64\u2013122","journal-title":"Foot Ankle"},{"key":"1635_CR17","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/ajcp\/45.4_ts.493","volume":"45","author":"AW Bauer","year":"1966","unstructured":"Bauer AW, Kirby WM, Sherris JC, Turck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Patholo 45:493\u2013496","journal-title":"Am J Clin Patholo"},{"key":"1635_CR18","unstructured":"Clinical and Laboratory Standards Institute (2007) Performance standards for antimicrobial susceptibility testing: Seventeenth informational supplement. Wayne, PA, pp\u00a0M100\u2013S17"},{"key":"1635_CR19","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1128\/AAC.39.1.185","volume":"39","author":"C Levesque","year":"1995","unstructured":"Levesque C, Piche L, Larose C, Roy P (1995) PCR mapping of integrons reveals several novel combinations of resistance genes. Antimicrob Agents Chemother 39:185\u2013191","journal-title":"Antimicrob Agents Chemother"},{"key":"1635_CR20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2006-7-s1-s10","volume":"7","author":"V Solovyev","year":"2006","unstructured":"Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7:1\u201310","journal-title":"Genome Biol"},{"key":"1635_CR21","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1093\/nar\/gki442","volume":"33","author":"E Quevillon","year":"2005","unstructured":"Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:116\u2013120","journal-title":"Nucleic Acids Res"},{"key":"1635_CR22","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673\u20134680","journal-title":"Nucleic Acids Res"},{"key":"1635_CR23","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1093\/molbev\/msm092","volume":"24","author":"K Tamura","year":"2007","unstructured":"Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biol Evol 24:1596\u20131599","journal-title":"Molecular Biol Evol"},{"key":"1635_CR24","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1093\/bioinformatics\/14.1.48","volume":"14","author":"TL Bailey","year":"1998","unstructured":"Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14:48\u201354","journal-title":"Bioinformatics"},{"key":"1635_CR25","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1093\/nar\/gkl198","volume":"34","author":"TL Bailey","year":"2006","unstructured":"Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:369\u2013373","journal-title":"Nucleic Acids Res"},{"key":"1635_CR26","first-page":"262","volume":"32","author":"YD Gao","year":"2011","unstructured":"Gao YD, Huang JF (2011) An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level (in Chinese). Zool Res 32:262\u2013266","journal-title":"Zool Res"},{"key":"1635_CR27","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1093\/bioinformatics\/bti770","volume":"22","author":"K Arnold","year":"2006","unstructured":"Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL Workspace: a web-based environment for protein structure homology modeling. Bioinformatics 22:195\u2013201","journal-title":"Bioinformatics"},{"key":"1635_CR28","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1093\/nar\/gkg520","volume":"31","author":"T Schwede","year":"2003","unstructured":"Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31:3381\u20133385","journal-title":"Nucleic Acids Res"},{"key":"1635_CR29","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/nar\/gki001","volume":"33","author":"RA Laskowski","year":"2005","unstructured":"Laskowski RA, Chistyakov VV, Thornton JM (2005) D266-8 PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33:266\u2013268","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1635_CR30","doi-asserted-by":"crossref","first-page":"W590","DOI":"10.1093\/nar\/gkh477","volume":"1","author":"R Maiti","year":"2004","unstructured":"Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004) SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res 1(2):W590\u2013W594","journal-title":"Nucleic Acids Res"},{"key":"1635_CR31","first-page":"1","volume":"11","author":"Z Bikadi","year":"2009","unstructured":"Bikadi Z, Hazai E (2009) Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. J Chem Inf 11:1\u201315","journal-title":"J Chem Inf"},{"key":"1635_CR32","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1287\/moor.6.1.19","volume":"6","author":"FJ Solis","year":"1981","unstructured":"Solis FJ, Wets RJB (1981) Minimization by random search techniques. Math Operations Res 6:19\u201330","journal-title":"Math Operations Res"},{"key":"1635_CR33","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","volume":"19","author":"GM Morris","year":"1998","unstructured":"Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Arthur JO (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639\u20131662","journal-title":"J Comput Chem"},{"key":"1635_CR34","first-page":"1074","volume-title":"Manual of clinical microbiology","author":"LB Rice","year":"2003","unstructured":"Rice LB, Sahm D, Bonomo RA (2003) Mechanisms of resistance to antibacterial agents. In: Murray PR, Baron EJ, Pfaller MA, Jorgensen JH, Yolken RH (eds) Manual of clinical microbiology, 8th edn. ASM Press, Washington DC, pp\u00a01074\u20131101","edition":"8"},{"key":"1635_CR35","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1021\/bi901614m","volume":"49","author":"J Lee","year":"2010","unstructured":"Lee J, Yennawar NH, Gam J, Benkovic SJ (2010) Kinetic and structural characterization of dihydrofolate reductase from Streptococcus pneumoniae. Biochemistry 49:195\u2013206","journal-title":"Biochemistry"},{"key":"1635_CR36","doi-asserted-by":"crossref","unstructured":"She Q, Singh RK, Confalonieri F et al. (2007) Crystal structure of a putative nucleotidyltransferase (AAK41883.1) from Sulfolobus solfataricus at 1.40 \u00c5 resolution. Joint Center for Structural Genomics Submitted to the PDB data bank, doi: 10.2210\/pdb2rff\/pdb","DOI":"10.2210\/pdb2rff\/pdb"},{"key":"1635_CR37","doi-asserted-by":"crossref","first-page":"3609","DOI":"10.1021\/bi200067t","volume":"50","author":"J Feeney","year":"2011","unstructured":"Feeney J, Birdsall B, Kovalevskaya NV, Smurnyy YD, Navarro Peran EM, Polshakov VI (2011) NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions. Biochemistry 50:3609\u20133620","journal-title":"Biochemistry"},{"key":"1635_CR38","doi-asserted-by":"crossref","first-page":"4303","DOI":"10.1021\/bi982728m","volume":"38","author":"V Cody","year":"1999","unstructured":"Cody V, Galitsky N, Rak D, Luft JR, Pangborn W, Queener SF (1999) Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+. Biochemistry 38:4303\u20134312","journal-title":"Biochemistry"},{"key":"1635_CR39","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1006\/jmbi.1997.1560","volume":"20","author":"AR Gargaro","year":"1998","unstructured":"Gargaro AR, Soteriou A, Frenkiel TA, Bauer CJ, Birdsall B, Polshakov VI, Barsukov IL, Roberts GC, Feeney J (1998) The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate. J Mol Biol 20:119\u2013134","journal-title":"J Mol Biol"},{"key":"1635_CR40","doi-asserted-by":"crossref","first-page":"471","DOI":"10.3233\/ISB-00375","volume":"8","author":"N Vidya","year":"2008","unstructured":"Vidya N, Vadivukkarasi B, Manivannan G, Anbarasu K (2008) Molecular modeling and docking studies of glutamate racemase in Vibrio vulnificus CMCP6. Silico Biol 8:471\u2013483","journal-title":"Silico Biol"},{"key":"1635_CR41","doi-asserted-by":"crossref","first-page":"13305","DOI":"10.1021\/bi00041a005","volume":"34","author":"LC Pedersen","year":"1995","unstructured":"Pedersen LC, Benning MM, Holden HM (1995) Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase. Biochemistry 34:13305\u201313311","journal-title":"Biochemistry"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-012-1635-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00894-012-1635-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-012-1635-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,19]],"date-time":"2025-04-19T12:59:46Z","timestamp":1745067586000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00894-012-1635-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,10,25]]},"references-count":41,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2013,3]]}},"alternative-id":["1635"],"URL":"https:\/\/doi.org\/10.1007\/s00894-012-1635-5","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,10,25]]}}}