{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T20:06:45Z","timestamp":1768421205808,"version":"3.49.0"},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2015,5,7]],"date-time":"2015-05-07T00:00:00Z","timestamp":1430956800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100004329","name":"Javna Agencija za Raziskovalno Dejavnost RS","doi-asserted-by":"publisher","award":["P1-0002, J1-6743, L1-6745"],"award-info":[{"award-number":["P1-0002, J1-6743, L1-6745"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Javna Agencija za Raziskovalno Dejavnost RS","doi-asserted-by":"publisher","award":["J1-6743"],"award-info":[{"award-number":["J1-6743"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Javna Agencija za Raziskovalno Dejavnost RS","doi-asserted-by":"publisher","award":["P1-0208, L1-6745, J1-6743"],"award-info":[{"award-number":["P1-0208, L1-6745, J1-6743"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2015,8]]},"DOI":"10.1007\/s10822-015-9847-2","type":"journal-article","created":{"date-parts":[[2015,5,6]],"date-time":"2015-05-06T09:45:56Z","timestamp":1430905556000},"page":"707-712","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Molecular dynamics to enhance structure-based virtual screening on cathepsin B"],"prefix":"10.1007","volume":"29","author":[{"given":"Mitja","family":"Ogrizek","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samo","family":"Turk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samo","family":"Le\u0161nik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Izidor","family":"Sosi\u010d","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Milan","family":"Hodo\u0161\u010dek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bojana","family":"Mirkovi\u0107","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janko","family":"Kos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Du\u0161anka","family":"Jane\u017ei\u010d","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stanislav","family":"Gobec","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janez","family":"Konc","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,5,7]]},"reference":[{"key":"9847_CR1","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0076-6879(81)80043-2","volume":"80","author":"AJ Barrett","year":"1981","unstructured":"Barrett AJ (1981) Cathepsin B, cathepsin H, and cathepsin L. Meth Enzymol 80:535\u2013561","journal-title":"Meth Enzymol"},{"key":"9847_CR2","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1515\/BC.2005.108","volume":"386","author":"V Hook","year":"2005","unstructured":"Hook V, Toneff T, Bogyo M et al (2005) Inhibition of cathepsin B reduces \u03b2-amyloid production in regulated secretory vesicles of neuronal chromaffin cells: evidence for cathepsin B as a candidate \u03b2-secretase of Alzheimer\u2019s disease. Biol Chem 386:1325","journal-title":"Biol Chem"},{"key":"9847_CR3","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1038\/nrc1949","volume":"6","author":"MM Mohamed","year":"2006","unstructured":"Mohamed MM, Sloane BF (2006) Cysteine cathepsins: multifunctional enzymes in cancer. Nat Rev Cancer 6:764\u2013775","journal-title":"Nat Rev Cancer"},{"key":"9847_CR4","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1074\/jbc.272.2.1197","volume":"272","author":"C Illy","year":"1997","unstructured":"Illy C, Quraishi O, Wang J et al (1997) Role of the occluding loop in cathepsin B activity. J Biol Chem 272:1197\u20131202","journal-title":"J Biol Chem"},{"key":"9847_CR5","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1074\/jbc.M003820200","volume":"276","author":"PC Almeida","year":"2001","unstructured":"Almeida PC, Nantes IL, Chagas JR et al (2001) Cathepsin B activity regulation heparin-like glycosaminoglycans protect human cathepsin B from alkaline ph-induced inactivation. J Biol Chem 276:944\u2013951","journal-title":"J Biol Chem"},{"key":"9847_CR6","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1002\/cmdc.201100098","volume":"6","author":"B Mirkovi\u0107","year":"2011","unstructured":"Mirkovi\u0107 B, Renko M, Turk S et al (2011) Novel mechanism of cathepsin B inhibition by antibiotic nitroxoline and related compounds. ChemMedChem 6:1351\u20131356","journal-title":"ChemMedChem"},{"key":"9847_CR7","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1021\/jm301544x","volume":"56","author":"I Sosi\u010d","year":"2013","unstructured":"Sosi\u010d I, Mirkovi\u0107 B, Arenz K et al (2013) Development of new cathepsin B inhibitors: combining bioisosteric replacements and structure-based design to explore the structure\u2013activity relationships of nitroxoline derivatives. J Med Chem 56:521\u2013533","journal-title":"J Med Chem"},{"key":"9847_CR8","doi-asserted-by":"crossref","first-page":"8461","DOI":"10.1021\/jm101020z","volume":"53","author":"P Ripphausen","year":"2010","unstructured":"Ripphausen P, Nisius B, Peltason L, Bajorath J (2010) Quo vadis, virtual screening? A comprehensive survey of prospective applications. J Med Chem 53:8461\u20138467","journal-title":"J Med Chem"},{"key":"9847_CR9","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10822-013-9644-8","volume":"27","author":"GM Sastry","year":"2013","unstructured":"Sastry GM, Adzhigirey M, Day T et al (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 27:221\u2013234","journal-title":"J Comput Aided Mol Des"},{"key":"9847_CR10","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1021\/ci200528d","volume":"52","author":"T Scior","year":"2012","unstructured":"Scior T, Bender A, Tresadern G et al (2012) Recognizing pitfalls in virtual screening: a critical review. J Chem Inf Model 52:867\u2013881","journal-title":"J Chem Inf Model"},{"key":"9847_CR11","doi-asserted-by":"crossref","first-page":"6789","DOI":"10.1021\/jm0608356","volume":"49","author":"N Huang","year":"2006","unstructured":"Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49:6789\u20136801","journal-title":"J Med Chem"},{"key":"9847_CR12","doi-asserted-by":"crossref","first-page":"6582","DOI":"10.1021\/jm300687e","volume":"55","author":"MM Mysinger","year":"2012","unstructured":"Mysinger MM, Carchia M, Irwin JJ, Shoichet BK (2012) Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem 55:6582\u20136594","journal-title":"J Med Chem"},{"key":"9847_CR13","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1021\/ci200117n","volume":"51","author":"SE Nichols","year":"2011","unstructured":"Nichols SE, Baron R, Ivetac A, McCammon JA (2011) Predictive power of molecular dynamics receptor structures in virtual screening. J Chem Inf Model 51:1439\u20131446","journal-title":"J Chem Inf Model"},{"key":"9847_CR14","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455\u2013461","journal-title":"J Comput Chem"},{"key":"9847_CR15","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1752-153X-2-5","volume":"2","author":"NM O\u2019Boyle","year":"2008","unstructured":"O\u2019Boyle NM, Morley C, Hutchison GR (2008) Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. Chem Cent J 2:5","journal-title":"Chem Cent J"},{"key":"9847_CR16","doi-asserted-by":"crossref","unstructured":"O'Boyle NM, Banck M, James CA et al (2011) Open Babel: an open chemical toolbox. J Cheminf 3:33","DOI":"10.1186\/1758-2946-3-33"},{"key":"9847_CR17","unstructured":"Landrum G (2006) RDKit: open-source cheminformatics. (Online). http:\/\/www.rdkit.org . Accessed 03\/04\/2012"},{"key":"9847_CR18","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","author":"BR Brooks","year":"2009","unstructured":"Brooks BR, Brooks CL, MacKerell AD et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545\u20131614","journal-title":"J Comput Chem"},{"key":"9847_CR19","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen WL, Chandrasekhar J, Madura JD et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926\u2013935","journal-title":"J Chem Phys"},{"key":"9847_CR20","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1002\/jcc.540161211","volume":"16","author":"D Jane\u017ei\u010d","year":"1995","unstructured":"Jane\u017ei\u010d D, Venable RM, Brooks BR (1995) Harmonic analysis of large systems. III. Comparison with molecular dynamics. J Comput Chem 16:1554\u20131566","journal-title":"J Comput Chem"},{"key":"9847_CR21","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1023\/A:1008193805436","volume":"14","author":"G Schaftenaar","year":"2000","unstructured":"Schaftenaar G, Noordik JH (2000) Molden: a pre-and post-processing program for molecular and electronic structures*. J Comput Aided Mol Des 14:123\u2013134","journal-title":"J Comput Aided Mol Des"},{"key":"9847_CR22","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","volume":"31","author":"K Vanommeslaeghe","year":"2010","unstructured":"Vanommeslaeghe K, Hatcher E, Acharya C et al (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all atom additive biological force fields. J Comput Chem 31:671\u2013690","journal-title":"J Comput Chem"},{"key":"9847_CR23","doi-asserted-by":"crossref","first-page":"3144","DOI":"10.1021\/ci300363c","volume":"52","author":"K Vanommeslaeghe","year":"2012","unstructured":"Vanommeslaeghe K, MacKerell AD Jr (2012) Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J Chem Inf Model 52:3144\u20133154","journal-title":"J Chem Inf Model"},{"key":"9847_CR24","doi-asserted-by":"crossref","first-page":"3155","DOI":"10.1021\/ci3003649","volume":"52","author":"K Vanommeslaeghe","year":"2012","unstructured":"Vanommeslaeghe K, Raman EP, MacKerell AD Jr (2012) Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J Chem Inf Model 52:3155\u20133168","journal-title":"J Chem Inf Model"},{"key":"9847_CR25","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph\u00a014:33\u201338","journal-title":"J Mol Graph"},{"key":"9847_CR26","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.jmgm.2013.01.003","volume":"41","author":"AS Karaboga","year":"2013","unstructured":"Karaboga AS, Petronin F, Marchetti G et al (2013) Benchmarking of HPCC: a novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments. J Mol Graph Model 41:20\u201330","journal-title":"J Mol Graph Model"},{"key":"9847_CR27","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1021\/ci034261e","volume":"44","author":"U Bor\u0161tnik","year":"2004","unstructured":"Bor\u0161tnik U, Hodo\u0161cek M, Janezic D (2004) Improving the performance of molecular dynamics simulations on parallel clusters. J Chem Inf Comput Sci 44:359\u2013364","journal-title":"J Chem Inf Comput Sci"},{"key":"9847_CR28","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1016\/S1359-6446(03)02831-9","volume":"8","author":"M Congreve","year":"2003","unstructured":"Congreve M, Carr R, Murray C, Jhoti H (2003) A \u201crule of three\u201dfor fragment-based lead discovery? Drug Discov Today 8:876\u2013877","journal-title":"Drug Discov Today"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-015-9847-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-015-9847-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-015-9847-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,8]],"date-time":"2024-06-08T20:52:03Z","timestamp":1717879923000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-015-9847-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,5,7]]},"references-count":28,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2015,8]]}},"alternative-id":["9847"],"URL":"https:\/\/doi.org\/10.1007\/s10822-015-9847-2","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,5,7]]}}}