{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T07:09:29Z","timestamp":1765609769662,"version":"3.41.0"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"6-8","license":[{"start":{"date-parts":[[2017,5,8]],"date-time":"2017-05-08T00:00:00Z","timestamp":1494201600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","award":["CTQ2016-79138-R","TIN2014-52211-C2-1-R"],"award-info":[{"award-number":["CTQ2016-79138-R","TIN2014-52211-C2-1-R"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Deutsche Forschungsgemeinschaft (DE)","award":["Collaborative Research Center SFB 716"],"award-info":[{"award-number":["Collaborative Research Center SFB 716"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Vis Comput"],"published-print":{"date-parts":[[2017,6]]},"DOI":"10.1007\/s00371-017-1397-2","type":"journal-article","created":{"date-parts":[[2017,5,8]],"date-time":"2017-05-08T11:28:48Z","timestamp":1494242928000},"page":"869-881","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Interactive GPU-based generation of solvent-excluded surfaces"],"prefix":"10.1007","volume":"33","author":[{"given":"Pedro","family":"Hermosilla","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Krone","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor","family":"Guallar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pere-Pau","family":"V\u00e1zquez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00c0lvar","family":"Vinacua","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timo","family":"Ropinski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,5,8]]},"reference":[{"key":"1397_CR1","doi-asserted-by":"crossref","unstructured":"Behley, J., Steinhage, V., Cremers, A.B.: Efficient radius neighbor search in three-dimensional point clouds. In: 2015 IEEE International Conference on Robotics and Automation (ICRA), pp. 3625\u20133630 (2015)","DOI":"10.1109\/ICRA.2015.7139702"},{"issue":"3","key":"1397_CR2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1145\/357306.357310","volume":"1","author":"JF Blinn","year":"1982","unstructured":"Blinn, J.F.: A generalization of algebraic surface drawing. ACM Trans. Graph. 1(3), 235\u2013256 (1982)","journal-title":"ACM Trans. Graph."},{"issue":"4","key":"1397_CR3","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.jmgm.2006.02.012","volume":"25","author":"T Can","year":"2006","unstructured":"Can, T., Chen, C.I., Wang, Y.F.: Efficient molecular surface generation using level-set methods. J. Mol. Graph. Model. 25(4), 442\u2013454 (2006)","journal-title":"J. Mol. Graph. Model."},{"issue":"5","key":"1397_CR4","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1107\/S0021889883010985","volume":"16","author":"ML Connolly","year":"1983","unstructured":"Connolly, M.L.: Analytical molecular surface calculation. J. Appl. Crystallogr. 16(5), 548\u2013558 (1983)","journal-title":"J. Appl. Crystallogr."},{"issue":"1","key":"1397_CR5","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1145\/174462.156635","volume":"13","author":"H Edelsbrunner","year":"1994","unstructured":"Edelsbrunner, H., M\u00fccke, E.P.: Three-dimensional alpha shapes. ACM Trans. Graph. 13(1), 43\u201372 (1994)","journal-title":"ACM Trans. Graph."},{"key":"1397_CR6","unstructured":"Green, S.: White paper: CUDA particles. Technical reports (2007)"},{"key":"1397_CR7","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1073\/pnas.75.1.303","volume":"75","author":"J Greer","year":"1978","unstructured":"Greer, J., Bush, B.L.: Macromolecular shape and surface maps by solvent exclusion. Proc. Natl. Acad. Sci. 75, 303\u2013307 (1978)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"2","key":"1397_CR8","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1109\/TVCG.2014.2350479","volume":"21","author":"S Grottel","year":"2015","unstructured":"Grottel, S., Krone, M., M\u00fcller, C., Reina, G., Ertl, T.: MegaMol\u2014a prototyping framework for particle-based visualization. IEEE Trans. Vis. Comput. Graph. 21(2), 201\u2013214 (2015)","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"issue":"3","key":"1397_CR9","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1111\/j.1467-8659.2005.00855.x","volume":"24","author":"M Hadwiger","year":"2005","unstructured":"Hadwiger, M., Sigg, C., Scharsach, H., Bhler, K., Gross, M.: Real-time ray-casting and advanced shading of discrete isosurfaces. Comput. Graph. Forum 24(3), 303\u2013312 (2005)","journal-title":"Comput. Graph. Forum"},{"key":"1397_CR10","first-page":"113","volume":"24","author":"P Hermosilla","year":"2015","unstructured":"Hermosilla, P., Guallar, V., Vinacua, A., V\u00e1zquez, P.: High quality illustrative effects for molecular rendering. Comput. Graph. 24, 113\u2013120 (2015)","journal-title":"Comput. Graph."},{"key":"1397_CR11","unstructured":"Hoetzlein, R.C.: Fast fixed-radius nearest neighbors: interactive million-particle fluids. In: GPU Technology Conference (2014)"},{"key":"1397_CR12","doi-asserted-by":"crossref","unstructured":"Jurcik, A., Parulek, J., Sochor, J., Kozlikova, B.: Accelerated visualization of transparent molecular surfaces in molecular dynamics. In: IEEE Pacific Visualization Symposium, pp. 112\u2013119 (2016)","DOI":"10.1109\/PACIFICVIS.2016.7465258"},{"key":"1397_CR13","doi-asserted-by":"crossref","unstructured":"Kozl\u00edkov\u00e1, B., Krone, M., Lindow, N., Falk, M., Baaden, M., Baum, D., Viola, I., Parulek, J., Hege, H.C.: Visualization of molecular structure: state of the art revisited. Comput. Graph. Forum (2016)","DOI":"10.1111\/cgf.13072"},{"issue":"6","key":"1397_CR14","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1109\/TVCG.2009.157","volume":"15","author":"M Krone","year":"2009","unstructured":"Krone, M., Bidmon, K., Ertl, T.: Interactive visualization of molecular surface dynamics. IEEE Trans. Vis. Comput. Graph. 15(6), 1391\u20131398 (2009)","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"1397_CR15","doi-asserted-by":"crossref","unstructured":"Krone, M., Grottel, S., Ertl, T.: Parallel contour-buildup algorithm for the molecular surface. In: IEEE Symposium on Biological Data Visualization, pp. 17\u201322 (2011)","DOI":"10.1109\/BioVis.2011.6094043"},{"key":"1397_CR16","first-page":"67","volume":"1","author":"M Krone","year":"2012","unstructured":"Krone, M., Stone, J.E., Ertl, T., Schulten, K.: Fast visualization of gaussian density surfaces for molecular dynamics and particle system trajectories. EuroVis-Short Pap. 1, 67\u201371 (2012)","journal-title":"EuroVis-Short Pap."},{"issue":"12","key":"1397_CR17","doi-asserted-by":"crossref","first-page":"2486","DOI":"10.1109\/TVCG.2014.2346404","volume":"20","author":"N Lindow","year":"2014","unstructured":"Lindow, N., Baum, D., Hege, H.C.: Ligand excluded surface: a new type of molecular surface. IEEE Trans. Vis. Comput. Graph. 20(12), 2486\u20132495 (2014)","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"issue":"3","key":"1397_CR18","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1111\/j.1467-8659.2009.01693.x","volume":"29","author":"N Lindow","year":"2010","unstructured":"Lindow, N., Baum, D., Prohaska, S., Hege, H.C.: Accelerated visualization of dynamic molecular surfaces. Comput. Graph. Forum 29(3), 943\u2013952 (2010)","journal-title":"Comput. Graph. Forum"},{"key":"1397_CR19","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1145\/37402.37422","volume":"21","author":"WE Lorensen","year":"1987","unstructured":"Lorensen, W.E., Cline, H.E.: Marching cubes: a high resolution 3D surface construction algorithm. ACM SIGGRAPH Comput. Graph. Interact. Tech. 21, 163\u2013169 (1987)","journal-title":"ACM SIGGRAPH Comput. Graph. Interact. Tech."},{"key":"1397_CR20","doi-asserted-by":"publisher","unstructured":"Parulek, J., Viola, I.: Implicit representation of molecular surfaces. In: 2012 IEEE Pacific Visualization Symposium, pp. 217\u2013224 (2012). doi: 10.1109\/PacificVis.2012.6183594","DOI":"10.1109\/PacificVis.2012.6183594"},{"issue":"13","key":"1397_CR21","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.: UCSF Chimera\u2014a visualization system for exploratory research and analysis. J. Comput. Chem. 25(13), 1605\u20131612 (2004)","journal-title":"J. Comput. Chem."},{"issue":"1","key":"1397_CR22","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1146\/annurev.bb.06.060177.001055","volume":"6","author":"FM Richards","year":"1977","unstructured":"Richards, F.M.: Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng. 6(1), 151\u2013176 (1977)","journal-title":"Ann. Rev. Biophys. Bioeng."},{"issue":"3","key":"1397_CR23","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y","volume":"38","author":"MF Sanner","year":"1996","unstructured":"Sanner, M.F., Olson, A.J., Spehner, J.C.: Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38(3), 305\u2013320 (1996)","journal-title":"Biopolymers"},{"issue":"1","key":"1397_CR24","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1109\/TVCG.2015.2467293","volume":"22","author":"R Sk\u00e5nberg","year":"2016","unstructured":"Sk\u00e5nberg, R., V\u00e1zquez, P.P., Guallar, V., Ropinski, T.: Real-time molecular visualization supporting diffuse interreflections and ambient occlusion. IEEE Trans. Vis. Comput. Graph. 22(1), 718\u2013727 (2016)","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"issue":"5","key":"1397_CR25","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1109\/TVCG.2006.115","volume":"12","author":"M Tarini","year":"2006","unstructured":"Tarini, M., Cignoni, P., Montani, C.: Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans. Vis. Comput. Graph. 12(5), 1237\u20131244 (2006)","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"1397_CR26","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1006\/jsbi.1996.0022","volume":"116","author":"M Totrov","year":"1995","unstructured":"Totrov, M., Abagyan, R.: The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 116, 138\u2013143 (1995)","journal-title":"J. Struct. Biol."},{"issue":"5","key":"1397_CR27","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1109\/38.310720","volume":"14","author":"A Varshney","year":"1994","unstructured":"Varshney, A., Brooks, F.P., Wright, W.V.: Linearly scalable computation of smooth molecular surfaces. IEEE Comput. Graph. Appl. 14(5), 19\u201325 (1994)","journal-title":"IEEE Comput. Graph. Appl."},{"issue":"12","key":"1397_CR28","doi-asserted-by":"crossref","first-page":"e8140","DOI":"10.1371\/journal.pone.0008140","volume":"4","author":"D Xu","year":"2009","unstructured":"Xu, D., Zhang, Y.: Generating triangulated macromolecular surfaces by Euclidean distance transform. PLoS ONE 4(12), e8140 (2009)","journal-title":"PLoS ONE"},{"key":"1397_CR29","doi-asserted-by":"crossref","unstructured":"Yu, Z.: A List-based method for fast generation of molecular surfaces. In: International Conference of the IEEE Engineering in Medicine and Biology Society, vol. 31, pp. 5909\u20135912 (2009)","DOI":"10.1109\/IEMBS.2009.5334843"}],"container-title":["The Visual Computer"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00371-017-1397-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00371-017-1397-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00371-017-1397-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T08:36:35Z","timestamp":1750235795000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00371-017-1397-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5,8]]},"references-count":29,"journal-issue":{"issue":"6-8","published-print":{"date-parts":[[2017,6]]}},"alternative-id":["1397"],"URL":"https:\/\/doi.org\/10.1007\/s00371-017-1397-2","relation":{},"ISSN":["0178-2789","1432-2315"],"issn-type":[{"type":"print","value":"0178-2789"},{"type":"electronic","value":"1432-2315"}],"subject":[],"published":{"date-parts":[[2017,5,8]]}}}