{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T04:59:59Z","timestamp":1778129999722,"version":"3.51.4"},"reference-count":64,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,10,16]],"date-time":"2017-10-16T00:00:00Z","timestamp":1508112000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,10,16]],"date-time":"2017-10-16T00:00:00Z","timestamp":1508112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The current molecular docking study provided the Free Energy of Binding (FEB) for the interaction (nanotoxicity) between VDAC mitochondrial channels of three species (VDAC1-<jats:italic>Mus musculus<\/jats:italic>, VDAC1<jats:italic>-Homo sapiens<\/jats:italic>, VDAC2<jats:italic>-Danio rerio<\/jats:italic>) with SWCNT-H, SWCNT-OH, SWCNT-COOH carbon nanotubes. The general results showed that the FEB values were statistically more negative (p\u2009&lt;\u20090.05) in the following order<jats:bold>: (<\/jats:bold>SWCNT-VDAC2-<jats:italic>Danio rerio<\/jats:italic>)\u2009&gt;\u2009(SWCNT-VDAC1-<jats:italic>Mus musculus<\/jats:italic>)\u2009&gt;\u2009(SWCNT-VDAC1-<jats:italic>Homo sapiens<\/jats:italic>)\u2009&gt;\u2009(ATP-VDAC). More negative FEB values for SWCNT-COOH and OH were found in VDAC2-<jats:italic>Danio rerio<\/jats:italic>when compared with VDAC1-<jats:italic>Mus musculus<\/jats:italic>and VDAC1<jats:italic>-Homo sapiens<\/jats:italic>(p\u2009&lt;\u20090.05). In addition,<jats:italic>a<\/jats:italic>significant correlation (0.66\u2009&gt;\u2009r<jats:sup>2<\/jats:sup>\u2009&gt;\u20090.97) was observed between<jats:italic>n<\/jats:italic>-Hamada index and VDAC nanotoxicity (or FEB) for the zigzag topologies of SWCNT-COOH and SWCNT-OH. Predictive Nanoparticles-Quantitative-Structure Binding-Relationship models (nano-QSBR) for strong and weak SWCNT-VDAC docking interactions were performed using Perturbation Theory, regression and classification models. Thus, 405 SWCNT-VDAC interactions were predicted using a nano-PT-QSBR classifications model with high accuracy, specificity, and sensitivity (73\u201398%) in training and validation series, and a maximum AUROC value of 0.978. In addition, the best regression model was obtained with Random Forest (R<jats:sup>2<\/jats:sup>of 0.833, RMSE of 0.0844), suggesting an excellent potential to predict SWCNT-VDAC channel nanotoxicity. All study data are available at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/doi.org\/10.6084\/m9.figshare.4802320.v2\">https:\/\/doi.org\/10.6084\/m9.figshare.4802320.v2<\/jats:ext-link>.<\/jats:p>","DOI":"10.1038\/s41598-017-13691-8","type":"journal-article","created":{"date-parts":[[2017,10,10]],"date-time":"2017-10-10T14:04:55Z","timestamp":1507644295000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Decrypting Strong and Weak Single-Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channels Using Molecular Docking and Perturbation Theory"],"prefix":"10.1038","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7061-0811","authenticated-orcid":false,"given":"Michael","family":"Gonz\u00e1lez-Durruthy","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7107-5024","authenticated-orcid":false,"given":"Adriano V.","family":"Werhli","sequence":"additional","affiliation":[]},{"given":"Vinicius","family":"Seus","sequence":"additional","affiliation":[]},{"given":"Karina S.","family":"Machado","sequence":"additional","affiliation":[]},{"given":"Alejandro","family":"Pazos","sequence":"additional","affiliation":[]},{"given":"Cristian R.","family":"Munteanu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9392-2797","authenticated-orcid":false,"given":"Humberto","family":"Gonz\u00e1lez-D\u00edaz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9463-3049","authenticated-orcid":false,"given":"Jos\u00e9 M.","family":"Monserrat","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,10,16]]},"reference":[{"key":"13691_CR1","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1038\/nsmb.2841","volume":"21","author":"OP Choudhary","year":"2014","unstructured":"Choudhary, O. P. et al. Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1. Nat. Struct. Mol. Biol. 21, 626\u2013632 (2014).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"13691_CR2","doi-asserted-by":"publisher","first-page":"15370","DOI":"10.1073\/pnas.0808115105","volume":"105","author":"M Bayrhuber","year":"2008","unstructured":"Bayrhuber, M. et al. Structure of the human voltage-dependent anion channel. Proc. Natl. Acad. Sci. USA 105, 15370\u201315375 (2008).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"13691_CR3","doi-asserted-by":"publisher","first-page":"17742","DOI":"10.1073\/pnas.0809634105","volume":"105","author":"R Ujwal","year":"2008","unstructured":"Ujwal, R. et al. The crystal structure of mouse VDAC1 at 2.3 A resolution reveals mechanistic insights into metabolite gating. Proc. Natl. Acad. Sci. USA 105, 17742\u201317747 (2008).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"13691_CR4","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1085\/jgp.200409154","volume":"124","author":"SF Okada","year":"2004","unstructured":"Okada, S. F. et al. Voltage-dependent anion channel-1 (VDAC-1) contributes to ATP release and cell volume regulation in murine cells. J. Gen. Physiol. 124, 513\u2013526 (2004).","journal-title":"J. Gen. Physiol."},{"issue":"Pt 2","key":"13691_CR5","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1042\/bj3410233","volume":"341","author":"M Crompton","year":"1999","unstructured":"Crompton, M. The mitochondrial permeability transition pore and its role in cell death. Biochem. J. 341(Pt 2), 233\u2013249 (1999).","journal-title":"Biochem. J."},{"key":"13691_CR6","doi-asserted-by":"publisher","first-page":"C12","DOI":"10.1152\/ajpcell.00314.2006","volume":"293","author":"R Scatena","year":"2007","unstructured":"Scatena, R., Bottoni, P., Botta, G., Martorana, G. E. & Giardina, B. The role of mitochondria in pharmacotoxicology: a reevaluation of an old, newly emerging topic. Am. J. Physiol. Cell Physiol. 293, C12\u201321 (2007).","journal-title":"Am. J. Physiol. Cell Physiol."},{"key":"13691_CR7","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1007\/s00109-007-0190-5","volume":"85","author":"Y Pi","year":"2007","unstructured":"Pi, Y., Goldenthal, M. J. & Marin-Garcia, J. Mitochondrial channelopathies in aging. J. Mol. Med. (Berl.) 85, 937\u2013951 (2007).","journal-title":"J. Mol. Med. (Berl.)"},{"key":"13691_CR8","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/j.yjmcc.2014.09.023","volume":"78","author":"P Bernardi","year":"2015","unstructured":"Bernardi, P. & Di Lisa, F. The mitochondrial permeability transition pore: molecular nature and role as a target in cardioprotection. J. Mol. Cell. Cardiol. 78, 100\u2013106 (2015).","journal-title":"J. Mol. Cell. Cardiol."},{"issue":"Pt A","key":"13691_CR9","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.mito.2014.07.009","volume":"19","author":"C Martel","year":"2014","unstructured":"Martel, C., Wang, Z. & Brenner, C. VDAC phosphorylation, a lipid sensor influencing the cell fate. Mitochondrion 19(Pt A), 69\u201377 (2014).","journal-title":"Mitochondrion"},{"key":"13691_CR10","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/j.nano.2008.04.003","volume":"4","author":"M Foldvari","year":"2008","unstructured":"Foldvari, M. & Bagonluri, M. Carbon nanotubes as functional excipients for nanomedicines: II. Drug delivery and biocompatibility issues. Nanomed. 4, 183\u2013200 (2008).","journal-title":"Nanomed."},{"key":"13691_CR11","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.taap.2012.03.023","volume":"261","author":"AA Shvedova","year":"2012","unstructured":"Shvedova, A. A., Pietroiusti, A., Fadeel, B. & Kagan, V. E. Mechanisms of carbon nanotube-induced toxicity: focus on oxidative stress. Toxicol. Appl. Pharmacol. 261, 121\u2013133 (2012).","journal-title":"Toxicol. Appl. Pharmacol."},{"key":"13691_CR12","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1038\/nprot.2016.051","volume":"11","author":"S Forli","year":"2016","unstructured":"Forli, S. et al. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols 11, 905\u2013919 (2016).","journal-title":"Nature Protocols"},{"key":"13691_CR13","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1002\/(SICI)1097-0134(1997)1+<221::AID-PROT30>3.0.CO;2-O","volume":"Suppl 1","author":"B Kramer","year":"1997","unstructured":"Kramer, B., Rarey, M. & Lengauer, T. CASP2 experiences with docking flexible ligands using FlexX. Proteins Suppl 1, 221\u2013225 (1997).","journal-title":"Proteins"},{"key":"13691_CR14","doi-asserted-by":"publisher","first-page":"2234","DOI":"10.1021\/jp807701h","volume":"113","author":"Y Deng","year":"2009","unstructured":"Deng, Y. & Roux, B. Computations of standard binding free energies with molecular dynamics simulations. J. Phys. Chem. B 113, 2234\u20132246 (2009).","journal-title":"J. Phys. Chem. B"},{"key":"13691_CR15","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1038\/nature03197","volume":"432","author":"BK Shoichet","year":"2004","unstructured":"Shoichet, B. K. Virtual screening of chemical libraries. Nature 432, 862\u2013865 (2004).","journal-title":"Nature"},{"key":"13691_CR16","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1016\/j.tiv.2012.05.010","volume":"26","author":"X Wang","year":"2012","unstructured":"Wang, X. et al. Multi-walled carbon nanotubes induce apoptosis via mitochondrial pathway and scavenger receptor. Toxicol. In Vitro 26, 799\u2013806 (2012).","journal-title":"Toxicol. In Vitro"},{"key":"13691_CR17","doi-asserted-by":"publisher","first-page":"1378","DOI":"10.1021\/es048729l","volume":"39","author":"G Jia","year":"2005","unstructured":"Jia, G. et al. Cytotoxicity of carbon nanomaterials: single-wall nanotube, multi-wall nanotube, and fullerene. Environ. Sci. Technol. 39, 1378\u20131383 (2005).","journal-title":"Environ. Sci. Technol."},{"key":"13691_CR18","doi-asserted-by":"publisher","DOI":"10.1039\/C6RA08883J","volume":"6","author":"M Gonzalez-Durruthy","year":"2016","unstructured":"Gonzalez-Durruthy, M. et al. Predicting the binding properties of single walled carbon nanotubes (SWCNT) with an ADP\/ATP mitochondrial carrier using molecular docking, chemoinformatics, and nano-QSBR perturbation theory. RSC Advances 6, 58680 (2016).","journal-title":"RSC Advances"},{"key":"13691_CR19","doi-asserted-by":"publisher","first-page":"103229","DOI":"10.1039\/C5RA14435C","volume":"5","author":"M Gonz\u00e1lez-Durruthy","year":"2015","unstructured":"Gonz\u00e1lez-Durruthy, M. et al. Mitoprotective activity of oxidized carbon nanotubes against mitochondrial swelling induced in multiple experimental conditions and predictions with new expected-value perturbation theory. RSC Adv. 5, 103229\u2013103245 (2015).","journal-title":"RSC Adv."},{"key":"13691_CR20","doi-asserted-by":"crossref","unstructured":"Gonz\u00e1lez-Durruthy, M. et al. QSPR\/QSAR-based Perturbation Theory approach and mechanistic electrochemical assays on carbon nanotubes with optimal properties against mitochondrial Fenton reaction experimentally induced by Fe2\u2009+\u2009-overload. 115, 312-330 (2017).","DOI":"10.1016\/j.carbon.2017.01.002"},{"key":"13691_CR21","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.ecoenv.2015.09.038","volume":"124","author":"AP Toropova","year":"2016","unstructured":"Toropova, A. P. et al. Nano-QSAR: Model of mutagenicity of fullerene as a mathematical function of different conditions. Ecotoxicol. Environ. Saf. 124, 32\u201336 (2016).","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"13691_CR22","doi-asserted-by":"publisher","DOI":"10.1007\/s11051-016-3564-1","volume":"18","author":"K Jagiello","year":"2016","unstructured":"Jagiello, K. et al. Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives. Journal of nanoparticle research: an interdisciplinary forum for nanoscale science and technology 18, 256 (2016).","journal-title":"Journal of nanoparticle research: an interdisciplinary forum for nanoscale science and technology"},{"key":"13691_CR23","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.jphotobiol.2014.12.020","volume":"152","author":"M Shahbazy","year":"2015","unstructured":"Shahbazy, M., Kompany-Zareh, M. & Najafpour, M. M. QSAR analysis for nano-sized layered manganese-calcium oxide in water oxidation: An application of chemometric methods in artificial photosynthesis. J. Photochem. Photobiol. B. 152, 146\u2013155 (2015).","journal-title":"J. Photochem. Photobiol. B."},{"key":"13691_CR24","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.jtbi.2017.01.012","volume":"416","author":"AP Toropova","year":"2017","unstructured":"Toropova, A. P. & Toropov, A. A. Nano-QSAR in cell biology: Model of cell viability as a mathematical function of available eclectic data. J. Theor. Biol. 416, 113\u2013118 (2017).","journal-title":"J. Theor. Biol."},{"key":"13691_CR25","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1007\/978-1-4939-6960-9_22","volume":"1601","author":"S Manganelli","year":"2017","unstructured":"Manganelli, S. & Benfenati, E. Nano-QSAR Model for Predicting Cell Viability of Human Embryonic Kidney Cells. Methods Mol. Biol. 1601, 275\u2013290 (2017).","journal-title":"Methods Mol. Biol."},{"key":"13691_CR26","doi-asserted-by":"publisher","first-page":"608","DOI":"10.2174\/1389557515666150219121652","volume":"15","author":"AP Toropova","year":"2015","unstructured":"Toropova, A. P. & Toropov, A. A. Mutagenicity: QSAR - quasi-QSAR - nano-QSAR. Mini Rev Med Chem 15, 608\u2013621 (2015).","journal-title":"Mini Rev Med Chem"},{"key":"13691_CR27","doi-asserted-by":"publisher","first-page":"7203","DOI":"10.1039\/C5NR08279J","volume":"8","author":"N Sizochenko","year":"2016","unstructured":"Sizochenko, N., Gajewicz, A., Leszczynski, J. & Puzyn, T. Causation or only correlation? Application of causal inference graphs for evaluating causality in nano-QSAR models. Nanoscale 8, 7203\u20137208 (2016).","journal-title":"Nanoscale"},{"key":"13691_CR28","doi-asserted-by":"publisher","first-page":"313","DOI":"10.3109\/17435390.2014.930195","volume":"9","author":"A Gajewicz","year":"2015","unstructured":"Gajewicz, A. et al. Towards understanding mechanisms governing cytotoxicity of metal oxides nanoparticles: hints from nano-QSAR studies. Nanotoxicology 9, 313\u2013325 (2015).","journal-title":"Nanotoxicology"},{"key":"13691_CR29","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1038\/nnano.2011.10","volume":"6","author":"T Puzyn","year":"2011","unstructured":"Puzyn, T. et al. Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles. Nature nanotechnology 6, 175\u2013178 (2011).","journal-title":"Nature nanotechnology"},{"key":"13691_CR30","doi-asserted-by":"publisher","first-page":"1713","DOI":"10.2174\/1568026611313140011","volume":"13","author":"H Gonzalez-Diaz","year":"2013","unstructured":"Gonzalez-Diaz, H. et al. General theory for multiple input-output perturbations in complex molecular systems. 1. Linear QSPR electronegativity models in physical, organic, and medicinal chemistry. Curr. Top. Med. Chem. 13, 1713\u20131741 (2013).","journal-title":"Curr. Top. Med. Chem."},{"key":"13691_CR31","doi-asserted-by":"publisher","first-page":"10623","DOI":"10.1039\/C4NR01285B","volume":"6","author":"F Luan","year":"2014","unstructured":"Luan, F. et al. Computer-aided nanotoxicology: assessing cytotoxicity of nanoparticles under diverse experimental conditions by using a novel QSTR-perturbation approach. Nanoscale 6, 10623\u201310630 (2014).","journal-title":"Nanoscale"},{"key":"13691_CR32","doi-asserted-by":"publisher","first-page":"193","DOI":"10.2217\/nnm.14.96","volume":"10","author":"A Speck-Planche","year":"2015","unstructured":"Speck-Planche, A., Kleandrova, V. V., Luan, F. & Cordeiro, M. N. Computational modeling in nanomedicine: prediction of multiple antibacterial profiles of nanoparticles using a quantitative structure-activity relationship perturbation model. Nanomedicine (Lond) 10, 193\u2013204 (2015).","journal-title":"Nanomedicine (Lond)"},{"key":"13691_CR33","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2721","volume":"4","author":"C Fernandez-Lozano","year":"2016","unstructured":"Fernandez-Lozano, C., Gestal, M., Munteanu, C. R., Dorado, J. & Pazos, A. A methodology for the design of experiments in computational intelligence with multiple regression models. PeerJ 4, e2721 (2016).","journal-title":"PeerJ"},{"key":"13691_CR34","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-5-9","volume":"5","author":"AL Teixeira","year":"2013","unstructured":"Teixeira, A. L., Leal, J. P. & Falcao, A. O. Random forests for feature selection in QSPR Models - an application for predicting standard enthalpy of formation of hydrocarbons. J Cheminform 5, 9 (2013).","journal-title":"J Cheminform"},{"key":"13691_CR35","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/j.drudis.2014.10.012","volume":"20","author":"A Lavecchia","year":"2015","unstructured":"Lavecchia, A. Machine-learning approaches in drug discovery: methods and applications. Drug Discov. Today 20, 318\u2013331 (2015).","journal-title":"Drug Discov. Today"},{"key":"13691_CR36","doi-asserted-by":"crossref","unstructured":"Smith, T. C. & Frank, E. In Statistical Genomics: Methods and Protocols 353\u2013378 (Springer, New York, NY; 2016).","DOI":"10.1007\/978-1-4939-3578-9_17"},{"key":"13691_CR37","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-015-0094-2","volume":"7","author":"G Tsiliki","year":"2015","unstructured":"Tsiliki, G. et al. RRegrs: an R package for computer-aided model selection with multiple regression models. J Cheminform 7, 46 (2015).","journal-title":"J Cheminform"},{"key":"13691_CR38","doi-asserted-by":"crossref","unstructured":"Bishop, C. M. Neural Networks for Pattern Recognition (Oxford University Press, USA, New York; 1995).","DOI":"10.1093\/oso\/9780198538493.001.0001"},{"key":"13691_CR39","doi-asserted-by":"publisher","first-page":"8093","DOI":"10.1021\/cr3004339","volume":"113","author":"M Shahlaei","year":"2013","unstructured":"Shahlaei, M. Descriptor selection methods in quantitative structure-activity relationship studies: a review study. Chem. Rev. 113, 8093\u20138103 (2013).","journal-title":"Chem. Rev."},{"key":"13691_CR40","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1021\/ci3005308","volume":"53","author":"CY Shao","year":"2013","unstructured":"Shao, C. Y. et al. Dependence of QSAR models on the selection of trial descriptor sets: a demonstration using nanotoxicity endpoints of decorated nanotubes. J. Chem. Inf. Model. 53, 142\u2013158 (2013).","journal-title":"J. Chem. Inf. Model."},{"key":"13691_CR41","first-page":"59","volume":"1","author":"F Torrens","year":"2005","unstructured":"Torrens, F. Periodic Properties of Carbon Nanotubes Based on the Chiral Vector. Internet Electron. J. Mol. Des. 1, 59\u201381 (2005).","journal-title":"Internet Electron. J. Mol. Des."},{"key":"13691_CR42","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevB.52.2723","volume":"52","author":"H Yorikawa","year":"1995","unstructured":"Yorikawa, H. & Muramatsu, S. Energy gaps of semiconducting nanotubules. Phys. Rev. B 52, 2723 (1995).","journal-title":"Phys. Rev. B"},{"key":"13691_CR43","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevB.63.073408","volume":"63","author":"A Kleiner","year":"2001","unstructured":"Kleiner, A. & Eggert, S. Band gaps of primary metallic carbon nanotubes. Phys Rev B. 63, 073408 (2001).","journal-title":"Phys Rev B."},{"key":"13691_CR44","doi-asserted-by":"publisher","first-page":"2361","DOI":"10.1126\/science.1078727","volume":"298","author":"SM Bachilo","year":"2002","unstructured":"Bachilo, S. M. et al. Structure-assigned optical spectra of single-walled carbon nanotubes. Science 298, 2361\u20132366 (2002).","journal-title":"Science"},{"key":"13691_CR45","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevB.72.205438","volume":"72","author":"J Maultzsch","year":"2005","unstructured":"Maultzsch, J., Telg, H., Reich, S. & Thomsen, C. Radial breathing mode of single-walled carbon nanotubes: Optical transition energies and chiral-index assignment. Phys. Rev. B 72, 205438 (2005).","journal-title":"Phys. Rev. B"},{"key":"13691_CR46","doi-asserted-by":"publisher","first-page":"9074","DOI":"10.1021\/nn203303c","volume":"5","author":"XR Xia","year":"2011","unstructured":"Xia, X. R. et al. Mapping the surface adsorption forces of nanomaterials in biological systems. ACS Nano 5, 9074\u20139081 (2011).","journal-title":"ACS Nano"},{"key":"13691_CR47","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1016\/j.tibs.2010.03.005","volume":"35","author":"S Hiller","year":"2010","unstructured":"Hiller, S., Abramson, J., Mannella, C., Wagner, G. & Zeth, K. The 3D structures of VDAC represent a native conformation. Trends Biochem. Sci. 35, 514\u2013521 (2010).","journal-title":"Trends Biochem. Sci."},{"key":"13691_CR48","doi-asserted-by":"publisher","unstructured":"Munteanu, C.R. D., results and models for nanoQSAR & docking of SWCNT with Mitochondrial VDAC, https:\/\/doi.org\/10.6084\/m9.figshare.4802320.v2 (2017)","DOI":"10.6084\/m9.figshare.4802320.v2"},{"key":"13691_CR49","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235\u2013242 (2000).","journal-title":"Nucleic Acids Res."},{"key":"13691_CR50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000763","volume":"6","author":"D Ting","year":"2010","unstructured":"Ting, D. et al. Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput. Biol. 6, e1000763 (2010).","journal-title":"PLoS Comput. Biol."},{"key":"13691_CR51","doi-asserted-by":"publisher","first-page":"W375","DOI":"10.1093\/nar\/gkm216","volume":"35","author":"IW Davis","year":"2007","unstructured":"Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375\u2013383 (2007).","journal-title":"Nucleic Acids Res."},{"key":"13691_CR52","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1002\/prot.22187","volume":"74","author":"CH da Silveira","year":"2009","unstructured":"da Silveira, C. H. et al. Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins 74, 727\u2013743 (2009).","journal-title":"Proteins"},{"key":"13691_CR53","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-298","volume":"11","author":"ZR Xie","year":"2010","unstructured":"Xie, Z. R. & Hwang, M. J. An interaction-motif-based scoring function for protein-ligand docking. BMC Bioinformatics 11, 298 (2010).","journal-title":"BMC Bioinformatics"},{"key":"13691_CR54","doi-asserted-by":"publisher","first-page":"50212","DOI":"10.1074\/jbc.M310216200","volume":"278","author":"KH Park","year":"2003","unstructured":"Park, K. H., Chhowalla, M., Iqbal, Z. & Sesti, F. Single-walled carbon nanotubes are a new class of ion channel blockers. J. Biol. Chem. 278, 50212\u201350216 (2003).","journal-title":"J. Biol. Chem."},{"key":"13691_CR55","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1161\/CIRCRESAHA.108.178970","volume":"103","author":"S Das","year":"2008","unstructured":"Das, S., Wong, R., Rajapakse, N., Murphy, E. & Steenbergen, C. Glycogen synthase kinase 3 inhibition slows mitochondrial adenine nucleotide transport and regulates voltage-dependent anion channel phosphorylation. Circ. Res. 103, 983\u2013991 (2008).","journal-title":"Circ. Res."},{"key":"13691_CR56","doi-asserted-by":"publisher","first-page":"9852","DOI":"10.1021\/jp504516a","volume":"118","author":"BP Weiser","year":"2014","unstructured":"Weiser, B. P., Salari, R., Eckenhoff, R. G. & Brannigan, G. Computational investigation of cholesterol binding sites on mitochondrial VDAC. J. Phys. Chem. B 118, 9852\u20139860 (2014).","journal-title":"J. Phys. Chem. B"},{"key":"13691_CR57","doi-asserted-by":"publisher","first-page":"1444","DOI":"10.1016\/j.bbamem.2011.10.025","volume":"1818","author":"KS McCommis","year":"2012","unstructured":"McCommis, K. S. & Baines, C. P. The role of VDAC in cell death: friend or foe? Biochim. Biophys. Acta 1818, 1444\u20131450 (2012).","journal-title":"Biochim. Biophys. Acta"},{"key":"13691_CR58","doi-asserted-by":"publisher","DOI":"10.1088\/0957-4484\/15\/5\/013","volume":"15","author":"CW Chen","year":"2004","unstructured":"Chen, C. W. & Lee, M. H. Dependence of work function on the geometries of single-walled carbon nanotubes. Nanotechnology 15, 480 (2004).","journal-title":"Nanotechnology"},{"key":"13691_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-016-0158-y","volume":"8","author":"S Latti","year":"2016","unstructured":"Latti, S., Niinivehmas, S. & Pentikainen, O. T. Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization. J Cheminform 8, 45 (2016).","journal-title":"J Cheminform"},{"key":"13691_CR60","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1021\/nl034428i","volume":"3","author":"RB Weisman","year":"2003","unstructured":"Weisman, R. B. & Bachilo, S. M. Dependence of optical transition energies on structure for single-walled carbon nanotubes in aqueous suspension: An empirical Kataura plot. Nano Lett. 3, 1235\u20131238 (2003).","journal-title":"Nano Lett."},{"key":"13691_CR61","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott, O. & Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455\u2013461 (2010).","journal-title":"J. Comput. Chem."},{"key":"13691_CR62","doi-asserted-by":"publisher","first-page":"1425","DOI":"10.1021\/ci025513z","volume":"42","author":"R Natarajan","year":"2002","unstructured":"Natarajan, R., Nirdosh, I., Basak, S. C. & Mills, D. R. QSAR modeling of flotation collectors using principal components extracted from topological indices. J. Chem. Inf. Comput. Sci. 42, 1425\u20131430 (2002).","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"13691_CR63","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1148\/radiology.143.1.7063747","volume":"143","author":"JA Hanley","year":"1982","unstructured":"Hanley, J. A. & McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29\u201336 (1982).","journal-title":"Radiology"},{"key":"13691_CR64","first-page":"27","volume":"29","author":"A Ciampi","year":"2005","unstructured":"Ciampi, A., Marcos, A. G. & Limas, M. C. Correspondence analysis and two-way clustering. SORT 29, 27\u201342 (2005).","journal-title":"SORT"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-13691-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-13691-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-13691-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T17:03:57Z","timestamp":1719507837000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-13691-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,16]]},"references-count":64,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["13691"],"URL":"https:\/\/doi.org\/10.1038\/s41598-017-13691-8","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10,16]]},"assertion":[{"value":"2 June 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 September 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 October 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"13271"}}