{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T05:56:52Z","timestamp":1790488612981,"version":"4.1.0"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2018,11,20]],"date-time":"2018-11-20T00:00:00Z","timestamp":1542672000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100009826","name":"University of Colombo","doi-asserted-by":"crossref","award":["AP\/3\/2\/2014\/RG\/01"],"award-info":[{"award-number":["AP\/3\/2\/2014\/RG\/01"]}],"id":[{"id":"10.13039\/501100009826","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1007\/s00894-018-3879-1","type":"journal-article","created":{"date-parts":[[2018,11,20]],"date-time":"2018-11-20T17:28:05Z","timestamp":1542734885000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Exploring the binding properties of agonists interacting with glucocorticoid receptor: an in silico approach"],"prefix":"10.1007","volume":"24","author":[{"given":"Samith","family":"Rathnayake","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha","family":"Weerasinghe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,11,20]]},"reference":[{"key":"3879_CR1","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1002\/cmdc.201000014","volume":"5","author":"AS Veleiro","year":"2010","unstructured":"Veleiro AS, Alvarez LD, Eduardo SL, Burton G (2010) Structure of the glucocorticoid receptor, a flexible protein that can adapt to different ligands. ChemMedChem 5:649\u2013659","journal-title":"ChemMedChem"},{"key":"3879_CR2","doi-asserted-by":"publisher","first-page":"1352","DOI":"10.1021\/jm800007w","volume":"51","author":"LD \u00c1lvarez","year":"2008","unstructured":"\u00c1lvarez LD, Mart\u00ed MA, Veleiro AS, Presman DM, Estrin DA, Pecci A, Burton G (2008) Exploring the molecular basis of action of the passive antiglucocorticoid 21-hydroxy-6,19-epoxyprogesterone. J Med Chem 51:1352\u20131360","journal-title":"J Med Chem"},{"key":"3879_CR3","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/S0092-8674(02)00817-6","volume":"110","author":"RK Bledsoe","year":"2002","unstructured":"Bledsoe RK, Montana VG, Stanley TB, Delves CJ, Apolito CJ, Mckee DD, Consler TG, Parks DJ, Stewart EL, Willson TM, Lambert MH, Moore JT, Pearce KH, Xu HE, Carolina N (2002) Crystal structure of the glucocorticoid receptor ligand binding domain reveals a novel mode of receptor dimerization and coactivator recognition. Cell 110:93\u2013105","journal-title":"Cell"},{"key":"3879_CR4","doi-asserted-by":"publisher","first-page":"1869","DOI":"10.1002\/cmdc.200800256","volume":"3","author":"LD \u00c1lvarez","year":"2008","unstructured":"\u00c1lvarez LD, Mart\u00ed MA, Veleiro AS, Misico RI, Estrin DA, Pecci A, Burton G (2008) Hemisuccinate of 21-Hydroxy-6,19-Epoxyprogesterone: a tissue-specific modulator of the glucocorticoid receptor. ChemMedChem 3:1869\u20131877","journal-title":"ChemMedChem"},{"key":"3879_CR5","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1002\/jat.1570","volume":"30","author":"GK Prasanth","year":"2010","unstructured":"Prasanth GK, Divya LM, Sadasivan C (2010) Bisphenol-A can bind to human glucocorticoid receptor as an agonist\u00a0: an in silico study. J Appl Toxicol 30:769\u2013774","journal-title":"J Appl Toxicol"},{"issue":"6","key":"3879_CR6","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1016\/j.bbamcr.2009.11.012","volume":"1803","author":"PC Echeverria","year":"2010","unstructured":"Echeverria PC, Picard D (2010) Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochim Biophys Acta 1803(6):641\u2013649","journal-title":"Biochim Biophys Acta"},{"key":"3879_CR7","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1042\/bj20030175","volume":"373","author":"C Wid\u00e9n","year":"2003","unstructured":"Wid\u00e9n C, Gustafsson J, Wikstr\u00f6m A (2003) Cytosolic glucocorticoid receptor interaction with nuclear factor- \u03ba B proteins in rat liver cells. Biochem J 373:211\u2013220","journal-title":"Biochem J"},{"key":"3879_CR8","doi-asserted-by":"publisher","first-page":"1905","DOI":"10.1016\/S0140-6736(09)60326-3","volume":"373","author":"PJ Barnes","year":"2009","unstructured":"Barnes PJ, Adcock IM (2009) Glucocorticoid resistance in inflammatory diseases. Lancet 373:1905\u20131917","journal-title":"Lancet"},{"key":"3879_CR9","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1210\/me.2011-0068","volume":"25","author":"JR Flammer","year":"2011","unstructured":"Flammer JR, Rogatsky I (2011) Minireview: glucocorticoids in autoimmunity: unexpected targets and mechanisms. Mol Endocrinol 25:1075\u20131086","journal-title":"Mol Endocrinol"},{"key":"3879_CR10","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/j.cytogfr.2007.01.005","volume":"18","author":"AC Liberman","year":"2007","unstructured":"Liberman AC, Druker J, Perone MJ, Arzt E (2007) Glucocorticoids in the regulation of transcription factors that control cytokine synthesis. Cytokine Growth Factor Rev 18:45\u201356","journal-title":"Cytokine Growth Factor Rev"},{"key":"3879_CR11","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1016\/j.ejphar.2007.11.076","volume":"583","author":"K Bosscher De","year":"2008","unstructured":"De Bosscher K, Van Craenenbroeck K, Meijer OC, Haegeman G (2008) Selective transrepression versus transactivation mechanisms by glucocorticoid receptor modulators in stress and immune systems. Eur J Pharmacol 583:290\u2013302","journal-title":"Eur J Pharmacol"},{"key":"3879_CR12","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/S1360-1385(00)01741-6","volume":"5","author":"E Pichersky","year":"2000","unstructured":"Pichersky E, Gang DR (2000) Genetics and biochemistry of secondary metabolites in plants\u00a0: an evolutionary perspective. Trends Plant Sci 5:439\u2013445","journal-title":"Trends Plant Sci"},{"key":"3879_CR13","unstructured":"Suk K (2007) Research focus on natural products and the body\u2019s immune and inflammatory systems. Nova Science, Hauppauge"},{"key":"3879_CR14","unstructured":"Herat T (2007) Endemic plants of Sri Lanka. Ministry of Environment and Natural Resources Sri Lanka"},{"key":"3879_CR15","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1016\/j.drudis.2015.01.003","volume":"20","author":"C Rakers","year":"2015","unstructured":"Rakers C, Bermudez M, Murgueitio MS, Riniker R, Wolber G (2015) The impact of molecular dynamics on drug design: applications for the characterization of ligand\u2013macromolecule complexes. Drug Discov Today 20:686\u2013702","journal-title":"Drug Discov Today"},{"key":"3879_CR16","unstructured":"Frisch GESMJ, Trucks GW, Schlegel HB, Robb BMMA, Cheeseman JR, Scalmani G, Barone V, Petersson HPHGA, Nakatsuji H, Caricato M, Li X, Izmaylov MHAF, Bloino J, Zheng G, Sonnenberg JL, Ehara TNM, Toyota K, Fukuda R, Hasegawa J, Ishida M, Honda JY, Kitao O, Nakai H, Vreven T, Montgomery JA, Peralta EBJE, Ogliaro F, Bearpark M, Heyd JJ, Kudin JNKN, Staroverov VN, Keith T, Kobayashi R, Raghavachari JTK, Rendell A, Burant JC, Iyengar SS, Cossi JBCM, Rega N, Millam JM, Klene M, Knox JE, Bakken RESV, Adamo C, Jaramillo J, Gomperts R, Yazyev JWOO, Austin AJ, Cammi R, Pomelli C, Martin GAVRL, Morokuma K, Zakrzewski VG, Salvador ADDP, Dannenberg JJ, Dapprich S, Farkas JCO, Foresman JB, Ortiz JV, Fox DJ (2009) Gaussian 09 revision C.01. Gaussian Inc., Wallingford"},{"issue":"1\u20133","key":"3879_CR17","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S0169-409X(00)00129-0","volume":"46","author":"CA Lipinski","year":"2001","unstructured":"Lipinski CA (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46(1\u20133):3\u201326","journal-title":"Adv Drug Deliv Rev"},{"key":"3879_CR18","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.ddtec.2004.11.007","volume":"1","author":"CA Lipinski","year":"2004","unstructured":"Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1:337\u2013341","journal-title":"Drug Discov Today Technol"},{"issue":"1","key":"3879_CR19","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/1758-2946-4-17","volume":"4","author":"MD Hanwell","year":"2004","unstructured":"Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2004) Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 4(1):17","journal-title":"J Cheminform"},{"key":"3879_CR20","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1551\u20131676","journal-title":"J Comput Chem"},{"key":"3879_CR21","doi-asserted-by":"publisher","first-page":"1132","DOI":"10.1002\/jcc.23905","volume":"36","author":"WJ Allen","year":"2015","unstructured":"Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC (2015) DOCK 6: impact of new features and current docking performance. J Comput Chem 36:1132\u20131156","journal-title":"J Comput Chem"},{"key":"3879_CR22","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1002\/jcc.20291","volume":"26","author":"D Spoel Van Der","year":"2005","unstructured":"Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701\u20131718","journal-title":"J Comput Chem"},{"key":"3879_CR23","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"B Hess","year":"2008","unstructured":"Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435\u2013447","journal-title":"J Chem Theory Comput"},{"key":"3879_CR24","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","volume":"29","author":"S Pronk","year":"2013","unstructured":"Pronk S, P\u00e1ll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, Van Der Spoel D, Hess B, Lindahl E (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29:845\u2013854","journal-title":"Bioinformatics"},{"key":"3879_CR25","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1007\/s00249-011-0700-9","volume":"40","author":"N Schmid","year":"2011","unstructured":"Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE, Van Gunsteren WF (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J 40:843\u2013856","journal-title":"Eur Biophys J"},{"key":"3879_CR26","first-page":"1355","volume":"D60","author":"AW Sch\u00fcttelkopf","year":"2004","unstructured":"Sch\u00fcttelkopf AW, van Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D60:1355\u20131363","journal-title":"Acta Crystallogr"},{"key":"3879_CR27","unstructured":"Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) In: Pullman B (ed) Intermolecular forces. Reidel, Dordrecht, p 331"},{"key":"3879_CR28","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"U Essmann","year":"1995","unstructured":"Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577\u20138593","journal-title":"J Chem Phys"},{"key":"3879_CR29","doi-asserted-by":"publisher","first-page":"3684","DOI":"10.1063\/1.448118","volume":"81","author":"HJC Berendsen","year":"1984","unstructured":"Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684\u20133690","journal-title":"J Chem Phys"},{"key":"3879_CR30","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","volume":"18","author":"B Hess","year":"1998","unstructured":"Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1998) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463\u20131472","journal-title":"J Comput Chem"},{"key":"3879_CR31","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1016\/S0968-0004(00)89080-5","volume":"20","author":"RA Sayle","year":"1995","unstructured":"Sayle RA, Milner-White EJ (1995) RASMOL: biomolecular graphics for all. Trends Biochem Sci 20:374\u2013376","journal-title":"Trends Biochem Sci"},{"key":"3879_CR32","doi-asserted-by":"publisher","first-page":"2778","DOI":"10.1021\/ci200227u","volume":"51","author":"RA Laskowski","year":"2011","unstructured":"Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51:2778\u20132786","journal-title":"J Chem Inf Model"},{"key":"3879_CR33","doi-asserted-by":"publisher","first-page":"1951","DOI":"10.1021\/ci500020m","volume":"54","author":"R Kumari","year":"2014","unstructured":"Kumari R, Kumar R, Lynn A (2014) G-mmpbsa - a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54:1951\u20131962","journal-title":"J Chem Inf Model"},{"key":"3879_CR34","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1006\/jmbi.1999.3371","volume":"295","author":"H Gohlke","year":"2000","unstructured":"Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 295:337\u2013356","journal-title":"J Mol Biol"},{"key":"3879_CR35","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1071\/CH16232","volume":"69","author":"AG Guruge","year":"2016","unstructured":"Guruge AG, Udawatte BC, Weerasinghe S (2016) An in silico approach of Coumarin-derived inhibitors for human DNA topoisomerase I. Aust J Chem 69:1005\u20131015","journal-title":"Aust J Chem"},{"issue":"3\u20135","key":"3879_CR36","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1016\/0039-128X(89)90031-7","volume":"53","author":"VC Shah","year":"1989","unstructured":"Shah VC, D\u2019sa AS, De Souza NJ (1989) Chonemorphine, stigmasterol, and ecdysterone: steroids isolated through bioassay-directed plant screening programs. Steroids 53(3\u20135):559\u2013565","journal-title":"Steroids"},{"key":"3879_CR37","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1007\/BF00534928","volume":"74","author":"DK Chatterjee","year":"1987","unstructured":"Chatterjee DK, Iyer N, Ganguli BN (1987) Antiamoebic activity of chonemorphine, a steroidal alkaloid, in experimental models. Parasitol Res 74:30\u201333","journal-title":"Parasitol Res"},{"key":"3879_CR38","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1021\/np50052a026","volume":"50","author":"V Shah","year":"1987","unstructured":"Shah V, Sunder R, De Souza NJ (1987) Chonemorphine and rapanone\u2014antiparasitic agents from plant sources. J Nat Prod 50:730\u2013731","journal-title":"J Nat Prod"},{"issue":"6","key":"3879_CR39","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1002\/cbic.200400361","volume":"6","author":"J Langen Von","year":"2005","unstructured":"Von Langen J, Fritzemeier K, Diekmann S, Hillisch A (2005) Molecular basis of the interaction specificity between the human glucocorticoid receptor and its endogenous steroid ligand cortisol. Chembiochem 6(6):1110\u20131118","journal-title":"Chembiochem"},{"key":"3879_CR40","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch W, Sander C (1983) Dicionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577\u20132637","journal-title":"Biopolymers"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00894-018-3879-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-018-3879-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-018-3879-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,19]],"date-time":"2019-11-19T19:23:33Z","timestamp":1574191413000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00894-018-3879-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,20]]},"references-count":40,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["3879"],"URL":"https:\/\/doi.org\/10.1007\/s00894-018-3879-1","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,11,20]]},"assertion":[{"value":"15 April 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 November 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 November 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"342"}}