{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T01:37:57Z","timestamp":1763429877292,"version":"build-2065373602"},"reference-count":69,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T00:00:00Z","timestamp":1678147200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004681","name":"Higher Education Commission","doi-asserted-by":"publisher","award":["NRPU-3857"],"award-info":[{"award-number":["NRPU-3857"]}],"id":[{"id":"10.13039\/501100004681","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Vice Chancellor Seed Funding Initiative","award":["NRPU-3857"],"award-info":[{"award-number":["NRPU-3857"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Diffuse Large B-Cell Lymphoma (DLBCL) is the most common form of non-Hodgkin\u2019s lymphoma (NHL). Elevated expression of c-MYC in DLBCL is associated with poor prognosis of the disease. In different cancers, c-MYC has been found regulated by different ubiquitin-specific proteases (USPs), but to date, the role of USPs in c-MYC regulation has not been investigated in DLBCL. In this study, in situ co expression of c-MYC and three candidates USPs, USP28, USP36 and USP37, have been investigated in both the ABC and GCB subtypes of DLBCL. This shows that USP37 expression is positively correlated with the c-MYC expression in the ABC subtype of DLBCL. Structurally, both c-MYC and USP37 has shown large proportion of intrinsically disordered regions, minimizing their chances for full structure crystallization. Peptide array and docking simulations has shown that N-terminal region of c-MYC interacts directly with residues within and in proximity of catalytically active C19 domain of the USP37. Given the structural properties of the interaction sites in the c-MYC-USP37 complex, a peptidyl inhibitor has been designed. Molecular docking has shown that the peptide fits well in the targeted site of c-MYC, masking most of its residues involved in the binding with USP37. The findings could further be exploited to develop therapeutic interventions against the ABC subtype of DLBCL.<\/jats:p>","DOI":"10.3390\/molecules28062441","type":"journal-article","created":{"date-parts":[[2023,3,8]],"date-time":"2023-03-08T02:08:14Z","timestamp":1678241294000},"page":"2441","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Investigating In Situ Expression of c-MYC and Candidate Ubiquitin-Specific Proteases in DLBCL and Assessment for Peptidyl Disruptor Molecule against c-MYC-USP37 Complex"],"prefix":"10.3390","volume":"28","author":[{"given":"Durr e Sameen","family":"Kamran","sequence":"first","affiliation":[{"name":"Department of Pathology, Dow Ishrat-ul-Ebad Khan Institute of Oral Health Sciences, Dow University of Health Sciences, Karachi 75330, Pakistan"},{"name":"Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi 75330, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8862-179X","authenticated-orcid":false,"given":"Mushtaq","family":"Hussain","sequence":"additional","affiliation":[{"name":"Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi 75330, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Talat","family":"Mirza","sequence":"additional","affiliation":[{"name":"Department of Research, Ziauddin University, Karachi 75000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"66","DOI":"10.4103\/2278-330X.126531","article-title":"Management of relapsed-refractory diffuse large B cell lymphoma","volume":"3","author":"Raut","year":"2014","journal-title":"South Asian J. Cancer"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"394","DOI":"10.3322\/caac.21492","article-title":"Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"68","author":"Khazaei","year":"2018","journal-title":"CA Cancer J. Clin."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1038\/s41375-022-01620-2","article-title":"The 5th edition of the World Health Organization classification of haematolymphoid tumours: Lymphoid neoplasms","volume":"36","author":"Alaggio","year":"2022","journal-title":"Leukemia"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1182\/blood-2003-05-1545","article-title":"Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray","volume":"103","author":"Hans","year":"2004","journal-title":"Blood"},{"key":"ref_5","first-page":"195","article-title":"Molecular classification and treatment of diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma","volume":"26","author":"Roschewski","year":"2020","journal-title":"J. Caner"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1002\/ajh.26151","article-title":"2021 Update on Diffuse large B cell lymphoma: A review of current data and potential applications on risk stratification and management","volume":"96","author":"Barta","year":"2021","journal-title":"Am. J. Hematol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.pathol.2017.09.006","article-title":"Diffuse large B-cell lymphoma","volume":"50","author":"Li","year":"2018","journal-title":"Pathology"},{"key":"ref_8","first-page":"10","article-title":"Genetic and epigenetic determinants of diffuse large B-cell lymphoma","volume":"4","author":"Bakhshi","year":"2020","journal-title":"Blood Cancer J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"447","DOI":"10.5581\/1516-8484.20120111","article-title":"Pathophysiology and molecular aspects of diffuse large B-cell lymphoma","volume":"34","author":"Gouveia","year":"2012","journal-title":"Rev. Bras. Hematol. Hemoter."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1111\/j.1365-2141.2010.08159.x","article-title":"Advances in the understanding of MYC-induced lymphomagenesis","volume":"149","author":"Klapproth","year":"2010","journal-title":"Br. J. Haematol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1101\/gad.1067003","article-title":"Genomic targets of the human c-Myc protein","volume":"17","author":"Fernandez","year":"2003","journal-title":"Genes Dev."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1136\/jclinpath-2018-205075","article-title":"A multicolour flow cytometric assay for c-MYC protein in B-cell lymphoma","volume":"71","author":"Alayed","year":"2018","journal-title":"J. Clin. Pathol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"610","DOI":"10.7150\/jca.34055","article-title":"JNK\/AP1 Pathway Regulates MYC Expression and BCR Signaling through Ig Enhancers in Burkitt Lymphoma Cells","volume":"11","author":"Ding","year":"2020","journal-title":"J. Cancer"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Fallah, Y., Brundage, J., Allegakoen, P., and Shajahan-Haq, A.N. (2017). MYC-driven pathways in breast cancer subtypes. Biomolecules, 7.","DOI":"10.3390\/biom7030053"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1073\/pnas.1814027116","article-title":"Mutational landscape of primary, metastatic, and recurrent ovarian cancer reveals c-MYC gains as potential target for BET inhibitors","volume":"116","author":"Li","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Nguyen, L., Papenhausen, P., and Shao, H. (2017). The Role of c-MYC in B-Cell Lymphomas: Diagnostic and Molecular Aspects. Genes, 8.","DOI":"10.3390\/genes8040116"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1007\/s00262-020-02708-3","article-title":"Patterns of immune checkpoint protein expression in MYC-overexpressing aggressive B-cell non-Hodgkin lymphomas","volume":"70","author":"Landsburg","year":"2021","journal-title":"Cancer Immunol. Immunother."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1111\/apm.12390","article-title":"MYC protein expression is associated with poor prognosis in primary diffuse large B-cell lymphoma of the central nervous system","volume":"123","author":"Tapia","year":"2015","journal-title":"APMIS"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"93998","DOI":"10.18632\/oncotarget.21501","article-title":"MYC overexpression with its prognostic and clinic-pathological significance in breast cancer","volume":"8","author":"Qu","year":"2017","journal-title":"Oncotarget"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"6267","DOI":"10.1038\/s41598-018-24631-5","article-title":"Prognostic significances of overexpression MYC and\/or BCL2 in R-CHOP-treated diffuse large B-cell lymphoma: A Systematic review and meta-analysis","volume":"19","author":"Li","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3664","DOI":"10.1002\/jcp.25841","article-title":"Deubiquitinating enzyme USP22 positively regulates c-Myc stability and tumorigenic activity in mammalian and breast cancer cells","volume":"232","author":"Kim","year":"2017","journal-title":"J. Cell Physiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1038\/ncb1601","article-title":"The ubiquitin-specific protease USP28 is required for MYC stability","volume":"9","author":"Popov","year":"2007","journal-title":"Nat. Cell Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3734","DOI":"10.1073\/pnas.1411713112","article-title":"The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc","volume":"112","author":"Sun","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3407","DOI":"10.1172\/JCI73733","article-title":"The deubiquitinase USP28 controls intestinal homeostasis and promotes colorectal cancer","volume":"124","author":"Diefenbacher","year":"2014","journal-title":"J. Clin. Investig."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1084\/jem.20151673","article-title":"Deubiquitinase USP13 maintains glioblastoma stem cells by antagonizing FBXL14-mediated Myc ubiquitination","volume":"214","author":"Fang","year":"2017","journal-title":"J. Exp. Med."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13046-021-01843-8","article-title":"USP16 regulates castration-resistant prostate cancer cell proliferation by deubiquitinating and stabilizing c-Myc","volume":"40","author":"Ge","year":"2021","journal-title":"J. Exp. Clin. Cancer Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3957","DOI":"10.1038\/onc.2014.327","article-title":"USP37 directly deubiquitinates and stabilizes c-Myc in lung cancer","volume":"34","author":"Pan","year":"2015","journal-title":"Oncogene"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1002\/1873-3468.14296","article-title":"The deubiquitinating enzyme USP17 regulates c-Myc levels and controls cell proliferation and glycolysis","volume":"596","author":"Nagasaka","year":"2022","journal-title":"FEBS Lett."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1053\/j.seminhematol.2015.01.009","article-title":"MYC alterations in diffuse large B-cell lymphomas","volume":"52","author":"Karube","year":"2015","journal-title":"Semin. Hematol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4021","DOI":"10.1182\/blood-2012-10-460063","article-title":"MYC\/BCL2 protein coexpression contributes to the inferior survival of activated B-cell subtype of diffuse large B-cell lymphoma and demonstrates high-risk gene expression signatures: A report from The International DLBCL Rituximab-CHOP Consortium Program","volume":"121","author":"Hu","year":"2013","journal-title":"Blood"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/modpathol.3800396","article-title":"Evaluation of immunophenotype in diffuse large B-cell lymphoma and its impact on prognosis","volume":"18","author":"Berglund","year":"2005","journal-title":"Modern Pathol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1056\/NEJMoa012914","article-title":"The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma","volume":"346","author":"Rosenwald","year":"2002","journal-title":"NEJM"},{"key":"ref_33","first-page":"78","article-title":"Frequency of Subgroups of Diffuse Large B-Cell Lymphoma by Immunohistochemistry","volume":"14","author":"Bukhari","year":"2015","journal-title":"J. Liaquat Uni. Med. Health Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"6351","DOI":"10.1200\/JCO.2005.05.012","article-title":"Molecular pathogenesis of diffuse large B-cell lymphoma","volume":"23","author":"Lossos","year":"2005","journal-title":"J. Clin. Oncol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1159\/000505892","article-title":"The Spectrum of MYC Alterations in Diffuse Large B-Cell Lymphoma","volume":"143","author":"Xia","year":"2020","journal-title":"Acta Haematol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"15","DOI":"10.4103\/jpi.jpi_82_18","article-title":"Introduction to digital image analysis in whole-slide imaging: A white paper from the digital pathology association","volume":"10","author":"Aeffner","year":"2019","journal-title":"J. Pathol. Inform."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1097\/PAP.0000000000000263","article-title":"Clinical application of image analysis in pathology","volume":"27","author":"Cornish","year":"2020","journal-title":"Adv. Anat. Pathol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1159\/000521149","article-title":"Digital technology in diagnostic breast pathology and immunohistochemistry","volume":"89","author":"Rakha","year":"2022","journal-title":"Pathobiology"},{"key":"ref_39","first-page":"607","article-title":"Comparison of Manual and Digital Assessment of KI-67 in Neuroendocrine Tumors","volume":"156","author":"Raju","year":"2020","journal-title":"Am. J. Clin. Pathol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1016\/j.prp.2018.07.002","article-title":"Digital image analysis of pan-cytokeratin stained tumor slides for evaluation of tumor budding in pT1\/pT2 colorectal cancer: Results of a feasibility study","volume":"214","author":"Jepsen","year":"2018","journal-title":"Pathol. Res. Pract."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Lee, K.S., Kwak, Y., Nam, K.H., Kim, D.W., Kang, S.B., Choe, G., Kim, W.H., and Lee, H.S. (2016). Favorable prognosis in colorectal cancer patients with co-expression of c-MYC and \u00df-catenin. BMC Cancer, 16.","DOI":"10.1186\/s12885-016-2770-7"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"325","DOI":"10.4103\/jomfp.JOMFP_197_18","article-title":"Bcl-2 and c-Myc expression in oral dysplasia and oral squamous cell carcinoma: An immunohistochemical study to assess tumor progression","volume":"22","author":"Pallavi","year":"2018","journal-title":"J. Oral Maxillofac. Pathol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1177\/1947601910378691","article-title":"MYC and Breast Cancer","volume":"1","author":"Xu","year":"2010","journal-title":"Genes Cancer"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Lin, C.N., Wang, C.J., Chao, Y.J., Lai, M.D., and Shan, Y.S. (2015). The significance of the co-existence of osteopontin and tumor-associated macrophages in gastric cancer progression. BMC Cancer, 15.","DOI":"10.1186\/s12885-015-1114-3"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1111\/vco.12190","article-title":"PDGFRs expression in dogs affected by malignant oral melanomas: Correlation with prognosis","volume":"15","author":"Iussich","year":"2017","journal-title":"Vet. Comp. Oncol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.eururo.2004.04.008","article-title":"Hypoxia-Inducible Factor 1\u00ce\u00b1 Expression Corre-lates with Angiogenesis and Unfavorable Prognosis in Bladder Cancer","volume":"46","author":"Theodoropoulos","year":"2004","journal-title":"Eur. Urol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1021\/acs.analchem.7b04380","article-title":"Peptide Arrays: Development and Application","volume":"90","author":"Szymczak","year":"2018","journal-title":"Anal. Chem."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"170898","DOI":"10.1016\/j.peptides.2022.170898","article-title":"A peptide array pipeline for the development of Spike-ACE2 interaction inhibitors","volume":"158","author":"Chopra","year":"2022","journal-title":"Peptides"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"3920","DOI":"10.1021\/acs.jpcb.8b01763","article-title":"Accurately Predicting Disordered Regions of Proteins Using Rosetta Residue Disorder Application","volume":"122","author":"Kim","year":"2018","journal-title":"J. Phys. Chem. B"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1016\/j.molcel.2018.09.031","article-title":"MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis","volume":"72","author":"Kalkat","year":"2018","journal-title":"Mol. Cell"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Allevato, M., Bolotin, E., Grossman, M., Mane-Padros, D., Sladek, F.M., and Martinez, E. (2017). Sequence-specific DNA binding by MYC\/MAX to low-affinity non-E-box motifs. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0180147"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"a014357","DOI":"10.1101\/cshperspect.a014357","article-title":"An overview of MYC and its interactome","volume":"4","author":"McFerrin","year":"2014","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"106769","DOI":"10.1016\/j.bpc.2022.106769","article-title":"Intrinsically disordered proteins\/regions and insight into their biomolecular interactions","volume":"283","author":"Chakrabarti","year":"2022","journal-title":"Biophys. Chem."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2423","DOI":"10.1128\/MCB.20.7.2423-2435.2000","article-title":"c-Myc proteolysis by the ubiquitin-proteasome pathway: Stabilization of c-Myc in Burkitt\u2019s lymphoma cells","volume":"20","author":"Gregory","year":"2000","journal-title":"Mol. Cell Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2854","DOI":"10.2174\/092986711796150496","article-title":"Peptides or small molecules? Different approaches to develop more effective CDK inhibitors","volume":"18","author":"Cirillo","year":"2011","journal-title":"Curr. Med. Chem."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"10930","DOI":"10.1021\/acs.analchem.0c02449","article-title":"The Utility of Native MS for Understanding the Mechanism of Action of Repurposed Therapeutics in COVID-19: Heparin as a Disruptor of the SARS-CoV-2 Interaction with Its Host Cell Receptor","volume":"92","author":"Yang","year":"2020","journal-title":"Anal. Chem."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Pobbati, A.V., and Rubin, B.P. (2020). Protein-Protein Interaction Disruptors of the YAP\/TAZ-TEAD Transcriptional Complex. Molecules, 25.","DOI":"10.3390\/molecules25246001"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Alkhashrom, S., Kicuntod, J., Stillger, K., L\u00fctzenburg, T., Anzenhofer, C., Neundorf, I., Marschall, M., and Eichler, J. (2022). A Peptide Inhibitor of the Human Cytomegalovirus Core Nuclear Egress Complex. Pharmaceuticals, 15.","DOI":"10.3390\/ph15091040"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1097\/PAI.0000000000000370","article-title":"IHC Optical Density Score: A New Practical Method for Quantitative Immunohistochemistry Image Analysis","volume":"25","author":"Jafari","year":"2017","journal-title":"Appl. Immunohistochem. Mol. Morphol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"The UniProt Consortium (2023). UniProt: The Universal Protein Knowledgebase in 2023. Nucleic Acids Res., 51, D523\u2013D531.","DOI":"10.1093\/nar\/gkac1052"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"D464","DOI":"10.1093\/nar\/gky1004","article-title":"RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy","volume":"47","author":"Burley","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"D265","DOI":"10.1093\/nar\/gkz991","article-title":"CDD\/SPARCLE: The conserved domain database in 2020","volume":"48","author":"Lu","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3403","DOI":"10.1093\/bioinformatics\/btm477","article-title":"XtalPred: A web server for prediction of protein crystallizability","volume":"23","author":"Slabinski","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-40"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/S0076-6879(03)74020-8","article-title":"Modeller: Generation and refinement of homology-based protein structure models","volume":"374","author":"Fiser","year":"2003","journal-title":"Methods Enzymol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: All-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: A protein-protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/btw514","article-title":"PRODIGY: A web server for predicting the binding affinity of protein\u2013protein complexes","volume":"32","author":"Xue","year":"2016","journal-title":"Bioinformatics"}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/28\/6\/2441\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:50:01Z","timestamp":1760122201000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/28\/6\/2441"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,7]]},"references-count":69,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,3]]}},"alternative-id":["molecules28062441"],"URL":"https:\/\/doi.org\/10.3390\/molecules28062441","relation":{},"ISSN":["1420-3049"],"issn-type":[{"type":"electronic","value":"1420-3049"}],"subject":[],"published":{"date-parts":[[2023,3,7]]}}}