{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T18:03:03Z","timestamp":1792000983026,"version":"4.4.0"},"reference-count":37,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010221","name":"Higher Education Commision, Pakistan","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010221","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Graphics and Modelling"],"published-print":{"date-parts":[[2025,3]]},"DOI":"10.1016\/j.jmgm.2024.108925","type":"journal-article","created":{"date-parts":[[2024,12,4]],"date-time":"2024-12-04T07:45:54Z","timestamp":1733298354000},"page":"108925","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"special_numbering":"C","title":["Unraveling Interleukin-1\u03b2 inhibition: Computational insights into anti-inflammatory compound selection for inflammatory disorders"],"prefix":"10.1016","volume":"135","author":[{"given":"Madiha","family":"Sardar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali Raza","family":"Siddiqui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadeem","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mamona","family":"Mushtaq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sehrish","family":"Shafeeq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Nur-e-Alam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Nabeel","family":"Ghayur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8530-8711","authenticated-orcid":false,"given":"Zaheer","family":"Ul-Haq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"10","key":"10.1016\/j.jmgm.2024.108925_bib1","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1038\/s41584-019-0277-8","article-title":"The IL-1 family of cytokines and receptors in rheumatic diseases","volume":"15","author":"Dinarello","year":"2019","journal-title":"Nat. Rev. Rheumatol."},{"key":"10.1016\/j.jmgm.2024.108925_bib2","series-title":"Immunoregulatory Role of Thymus","author":"Dabrowski","year":"2019"},{"key":"10.1016\/j.jmgm.2024.108925_bib3","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.3389\/fimmu.2019.01266","article-title":"Divergent roles for the IL-1 family in gastrointestinal homeostasis and inflammation","volume":"10","author":"McEntee","year":"2019","journal-title":"Front. Immunol."},{"issue":"4","key":"10.1016\/j.jmgm.2024.108925_bib4","first-page":"253","article-title":"Interleukin-1, Cytokine & growth factor reviews","volume":"8","author":"Dinarello","year":"1997"},{"key":"10.1016\/j.jmgm.2024.108925_bib5","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiolchem.2022.107774","article-title":"Interface inhibitory action on Interleukin-1\u03b2 using selected anti-inflammatory compounds to mitigate the depression: a computational investigation","volume":"101","author":"Sardar","year":"2022","journal-title":"Comput. Biol. Chem."},{"issue":"8","key":"10.1016\/j.jmgm.2024.108925_bib6","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1038\/s41584-022-00797-1","article-title":"IL-1 and autoinflammatory disease: biology, pathogenesis and therapeutic targeting","volume":"18","author":"Broderick","year":"2022","journal-title":"Nat. Rev. Rheumatol."},{"key":"10.1016\/j.jmgm.2024.108925_bib7","doi-asserted-by":"crossref","first-page":"167","DOI":"10.3389\/fimmu.2013.00167","article-title":"New insights in the immunobiology of IL-1 family members","volume":"4","author":"van de Veerdonk","year":"2013","journal-title":"Front. Immunol."},{"issue":"2","key":"10.1016\/j.jmgm.2024.108925_bib8","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1002\/j.1460-2075.1988.tb02818.x","article-title":"Crystal structure of the cytokine interleukin\u20101 beta","volume":"7","author":"Priestle","year":"1988","journal-title":"EMBO J."},{"issue":"3","key":"10.1016\/j.jmgm.2024.108925_bib9","doi-asserted-by":"crossref","first-page":"237","DOI":"10.4168\/aair.2017.9.3.237","article-title":"Anti-interleukin-9 antibody increases the effect of allergen-specific immunotherapy in murine allergic rhinitis","volume":"9","author":"Shin","year":"2017","journal-title":"Allergy, Asthma &; Immunol. Res."},{"issue":"6621","key":"10.1016\/j.jmgm.2024.108925_bib10","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1038\/386190a0","article-title":"Crystal structure of the type-I interleukin-1 receptor complexed with interleukin-1\u03b2","volume":"386","author":"Vigers","year":"1997","journal-title":"Nature"},{"key":"10.1016\/j.jmgm.2024.108925_bib11","series-title":"Chemical Computing Group Inc","year":"2016"},{"key":"10.1016\/j.jmgm.2024.108925_bib12","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.jmgm.2017.04.004","article-title":"Development of efficient docking strategies and structure-activity relationship study of the c-Met type II inhibitors","volume":"75","author":"Li","year":"2017","journal-title":"J. Mol. Graph. Model."},{"issue":"18","key":"10.1016\/j.jmgm.2024.108925_bib13","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.2174\/156802608786786624","article-title":"Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery","volume":"8","author":"Vilar","year":"2008","journal-title":"Curr. Top. Med. Chem."},{"issue":"11","key":"10.1016\/j.jmgm.2024.108925_bib14","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1021\/ci100241y","article-title":"Analyzing the topology of active sites: on the prediction of pockets and subpockets","volume":"50","author":"Volkamer","year":"2010","journal-title":"J. Chem. Inf. Model."},{"issue":"10","key":"10.1016\/j.jmgm.2024.108925_bib15","doi-asserted-by":"crossref","first-page":"3128","DOI":"10.1021\/acs.jcim.3c00336","article-title":"Binding site detection remastered: enabling fast, robust, and reliable binding site detection and descriptor calculation with DoGSite3","volume":"63","author":"Graef","year":"2023","journal-title":"J. Chem. Inf. Model."},{"issue":"16","key":"10.1016\/j.jmgm.2024.108925_bib16","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.2174\/1568026614666140929124445","article-title":"Structure-based virtual screening for drug discovery: principles, applications and recent advances","volume":"14","author":"Lionta","year":"2014","journal-title":"Curr. Top. Med. Chem."},{"issue":"10","key":"10.1016\/j.jmgm.2024.108925_bib17","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1021\/ci900263d","article-title":"Novel approach for efficient pharmacophore-based virtual screening: method and applications","volume":"49","author":"Dror","year":"2009","journal-title":"J. Chem. Inf. Model."},{"issue":"14","key":"10.1016\/j.jmgm.2024.108925_bib18","doi-asserted-by":"crossref","first-page":"6582","DOI":"10.1021\/jm300687e","article-title":"Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking","volume":"55","author":"Mysinger","year":"2012","journal-title":"J. Med. Chem."},{"issue":"Suppl 1","key":"10.1016\/j.jmgm.2024.108925_bib19","article-title":"Sensitivity, specificity, receiver-operating characteristic (ROC) curves and likelihood ratios: communicating the performance of diagnostic tests","volume":"29","author":"Florkowski","year":"2008","journal-title":"Clin. Biochem. Rev."},{"issue":"3","key":"10.1016\/j.jmgm.2024.108925_bib20","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1002\/qsar.19860050305","article-title":"Three\u2010dimensional quantitative structure\u2010activity relationships I. General approach to the pharmacophore model validation","volume":"5","author":"Motoc","year":"1986","journal-title":"Quant. Struct.-Act. Relat."},{"issue":"1","key":"10.1016\/j.jmgm.2024.108925_bib21","doi-asserted-by":"crossref","DOI":"10.1038\/srep42717","article-title":"SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules","volume":"7","author":"Daina","year":"2017","journal-title":"Sci. Rep."},{"issue":"16","key":"10.1016\/j.jmgm.2024.108925_bib22","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: fast, flexible, and free","volume":"26","author":"Van Der Spoel","year":"2005","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.jmgm.2024.108925_bib23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1756-0500-5-367","article-title":"ACPYPE-Antechamber python parser interface","volume":"5","author":"Sousa da Silva","year":"2012","journal-title":"BMC Res. Notes"},{"issue":"43","key":"10.1016\/j.jmgm.2024.108925_bib24","doi-asserted-by":"crossref","first-page":"9954","DOI":"10.1021\/jp003020w","article-title":"Structure and dynamics of the TIP3P, SPC, and SPC\/E water models at 298 K","volume":"105","author":"Mark","year":"2001","journal-title":"J. Phy. Chem. A"},{"issue":"1","key":"10.1016\/j.jmgm.2024.108925_bib25","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"issue":"13","key":"10.1016\/j.jmgm.2024.108925_bib26","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.jmgm.2024.108925_bib27","series-title":"XMGRACE, Version 5.1. 19, Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology","author":"Turner","year":"2005"},{"key":"10.1016\/j.jmgm.2024.108925_bib28","series-title":"Molecular Dynamics-Studies of Synthetic and Biological Macromolecules","first-page":"171","article-title":"MM-GB (PB) SA calculations of protein-ligand binding free energies","author":"Hayes","year":"2012"},{"issue":"7","key":"10.1016\/j.jmgm.2024.108925_bib29","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1021\/ci500020m","article-title":"g_mmpbsa\u2014 A GROMACS tool for high-throughput MM-PBSA calculations","volume":"54","author":"Kumari","year":"2014","journal-title":"J. Chem. Inf. Model."},{"issue":"1","key":"10.1016\/j.jmgm.2024.108925_bib30","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1002\/jccs.201900148","article-title":"Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson\u2013Boltzmann surface area methods","volume":"67","author":"Ren","year":"2020","journal-title":"J. Chin. Chem. Soc."},{"issue":"3","key":"10.1016\/j.jmgm.2024.108925_bib31","doi-asserted-by":"crossref","first-page":"793","DOI":"10.3390\/biomedicines11030793","article-title":"Identification of natural lead compounds against hemagglutinin-esterase surface glycoprotein in human coronaviruses investigated via MD simulation, principal component analysis, cross-correlation, H-bond plot and MMGBSA","volume":"11","author":"Ali","year":"2023","journal-title":"Biomedicines"},{"key":"10.1016\/j.jmgm.2024.108925_bib32","series-title":"Proceedings of the 15th python in Science Conference","doi-asserted-by":"crossref","first-page":"105","DOI":"10.25080\/Majora-629e541a-00e","article-title":"MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations","author":"Gowers","year":"2016"},{"issue":"3","key":"10.1016\/j.jmgm.2024.108925_bib33","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1002\/jcc.540160303","article-title":"The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies","volume":"16","author":"Eisenhaber","year":"1995","journal-title":"J. Comput. Chem."},{"issue":"8","key":"10.1016\/j.jmgm.2024.108925_bib34","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1038\/nrd3800","article-title":"Treating inflammation by blocking interleukin-1 in a broad spectrum of diseases","volume":"11","author":"Dinarello","year":"2012","journal-title":"Nat. Rev. Drug Discov."},{"issue":"13","key":"10.1016\/j.jmgm.2024.108925_bib35","doi-asserted-by":"crossref","first-page":"4885","DOI":"10.3390\/molecules28134885","article-title":"In silico identification of natural product-based inhibitors targeting IL-1\u03b2\/IL-1R protein\u2013protein interface","volume":"28","author":"Liu","year":"2023","journal-title":"Molecules"},{"key":"10.1016\/j.jmgm.2024.108925_bib36","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.compbiolchem.2015.06.004","article-title":"In silico identification of novel IL-1\u03b2 inhibitors to target protein\u2013protein interfaces","volume":"58","author":"Halim","year":"2015","journal-title":"Comput. Biol. Chem."},{"issue":"10","key":"10.1016\/j.jmgm.2024.108925_bib37","doi-asserted-by":"crossref","first-page":"2273","DOI":"10.1021\/np2003066","article-title":"Berkeleyones and related meroterpenes from a deep-water acid mine waste fungus that inhibit the production of interleukin 1-\u03b2 from induced inflammasomes","volume":"74","author":"Stierle","year":"2011","journal-title":"J. Nat. Prod."}],"container-title":["Journal of Molecular Graphics and Modelling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326324002250?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326324002250?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,2,12]],"date-time":"2025-02-12T08:57:36Z","timestamp":1739350656000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1093326324002250"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":37,"alternative-id":["S1093326324002250"],"URL":"https:\/\/doi.org\/10.1016\/j.jmgm.2024.108925","relation":{},"ISSN":["1093-3263"],"issn-type":[{"value":"1093-3263","type":"print"}],"subject":[],"published":{"date-parts":[[2025,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Unraveling Interleukin-1\u03b2 inhibition: Computational insights into anti-inflammatory compound selection for inflammatory disorders","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Graphics and Modelling","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmgm.2024.108925","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"108925"}}