{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T05:38:59Z","timestamp":1769837939720,"version":"3.49.0"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"S19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,11]]},"DOI":"10.1186\/1471-2105-14-s19-s5","type":"journal-article","created":{"date-parts":[[2013,11,12]],"date-time":"2013-11-12T07:05:10Z","timestamp":1384239910000},"source":"Crossref","is-referenced-by-count":27,"title":["Exploring cavity dynamics in biomolecular systems"],"prefix":"10.1186","volume":"14","author":[{"given":"Norbert","family":"Lindow","sequence":"first","affiliation":[]},{"given":"Daniel","family":"Baum","sequence":"additional","affiliation":[]},{"given":"Ana-Nicoleta","family":"Bondar","sequence":"additional","affiliation":[]},{"given":"Hans-Christian","family":"Hege","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,11,12]]},"reference":[{"issue":"6","key":"6189_CR1","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1085\/jgp.200910373","volume":"135","author":"RO Dror","year":"2010","unstructured":"Dror RO, Jensen M, Borhani DW, Shaw DE: Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J Gen Physiol. 2010, 135 (6): 555-562. 10.1085\/jgp.200910373. [\n                    http:\/\/dx.doi.org\/10.1085\/jgp.200910373\n                    \n                  ]","journal-title":"J Gen Physiol"},{"issue":"12","key":"6189_CR2","doi-asserted-by":"publisher","first-page":"2025","DOI":"10.1109\/TVCG.2011.259","volume":"17","author":"N Lindow","year":"2011","unstructured":"Lindow N, Baum D, Hege HC: Voronoi-Based Extraction and Visualization of Molecular Paths. IEEE Trans Vis Comput Graphics. 2011, 17 (12): 2025-2034.","journal-title":"IEEE Trans Vis Comput Graphics"},{"key":"6189_CR3","volume-title":"Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12)","author":"N Lindow","year":"2012","unstructured":"Lindow N, Baum D, Bondar AN, Hege HC: Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization. Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12). 2012"},{"key":"6189_CR4","volume-title":"Annu Rev Biophys Biomol Struct","author":"J Herzfeld","year":"2002","unstructured":"Herzfeld J, Lansing J: Magnetic resonance studies of the bacteriorhodopsin pump cycle. Annu Rev Biophys Biomol Struct. 2002, 31:"},{"issue":"2","key":"6189_CR5","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1016\/j.jmb.2003.10.068","volume":"335","author":"T Kouyama","year":"2004","unstructured":"Kouyama T, Nishikawa T, Tokuhisa T, Okumura H: Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle. Journal of Molecular Biology. 2004, 335 (2): 531-546. 10.1016\/j.jmb.2003.10.068.","journal-title":"Journal of Molecular Biology"},{"key":"6189_CR6","volume-title":"HOLE: a program for the analysis of the pore dimensions of ion channel structural models","author":"OS Smart","year":"1996","unstructured":"Smart OS, Neduvelil JG, Wang X, Wallace BA: HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph. 1996, 14 (6): [\n                    http:\/\/view.ncbi.nlm.nih.gov\/pubmed\/9195488\n                    \n                  ]"},{"key":"6189_CR7","doi-asserted-by":"publisher","first-page":"49+","DOI":"10.1186\/1472-6807-8-49","volume":"8","author":"BK Ho","year":"2008","unstructured":"Ho BK, Gruswitz F: HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct Biol. 2008, 8: 49+-10.1186\/1472-6807-8-49. [\n                    http:\/\/dx.doi.org\/10.1186\/1472-6807-8-49\n                    \n                  ]","journal-title":"BMC Struct Biol"},{"key":"6189_CR8","volume-title":"Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12)","author":"J Parulek","year":"2012","unstructured":"Parulek J, Turkay C, Reuter N, Viola I: Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations. Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12). 2012"},{"key":"6189_CR9","doi-asserted-by":"publisher","first-page":"316+","DOI":"10.1186\/1471-2105-7-316","volume":"7","author":"M Petr\u011bk","year":"2006","unstructured":"Petr\u011bk M, Otyepka M, Banas P, Kosinov\u00e1 P: CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics. 2006, 7: 316+-10.1186\/1471-2105-7-316. [\n                    http:\/\/dx.doi.org\/10.1186\/1471-2105-7-316\n                    \n                  ]","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"6189_CR10","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1016\/j.str.2007.10.007","volume":"15","author":"M Petr\u011bk","year":"2007","unstructured":"Petr\u011bk M, Kosinov\u00e1 P, Koca J, Otyepka M: MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure. 2007, 15 (11): 1357-1363. 10.1016\/j.str.2007.10.007. [\n                    http:\/\/www.sciencedirect.com\/science\/article\/B6VSR-4R46KGV-8\/2\/b0b51ca7cbaa1dbcbc15b3c9fd7fd0cb\n                    \n                  ]","journal-title":"Structure"},{"issue":"1-3","key":"6189_CR11","first-page":"107","volume":"15","author":"P Medek","year":"2007","unstructured":"Medek P, Bene\u0161 P, Sochor J: Computation of tunnels in protein molecules using Delaunay triangulation. J of WSCG. 2007, 15 (1-3): 107-114.","journal-title":"J of WSCG"},{"key":"6189_CR12","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1002\/prot.22052","volume":"73","author":"E Yaffe","year":"2008","unstructured":"Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R: MolAxis: Efficient and accurate identification of channels in macromolecules. Proteins: Struct, Funct, Bioinf. 2008, 73: 72-86. 10.1002\/prot.22052. [\n                    http:\/\/dx.doi.org\/10.1002\/prot.22052\n                    \n                  ]","journal-title":"Proteins: Struct, Funct, Bioinf"},{"key":"6189_CR13","volume-title":"J Mol Graph Model","author":"M Raunest","year":"2010","unstructured":"Raunest M, Kandt C: dxTuber: Detecting Protein Cavities, Tunnels and Clefts Based on Protein and Solvent Dynamics. J Mol Graph Model. 2010"},{"key":"6189_CR14","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1109\/BioVis.2011.6094043","volume-title":"Proc IEEE Symposium on Biological Data Visualization (BioVis 2011)","author":"M Krone","year":"2011","unstructured":"Krone M, Grottel S, Ertl T: Parallel Contour-Buildup Algorithm for the Molecular Surface. Proc IEEE Symposium on Biological Data Visualization (BioVis 2011). 2011, 17-22."},{"issue":"13","key":"6189_CR15","doi-asserted-by":"publisher","first-page":"1412","DOI":"10.1016\/j.cad.2005.02.013","volume":"37","author":"DS Kim","year":"2005","unstructured":"Kim DS, Cho Y, Kim D: Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Comput Aided Des. 2005, 37 (13): 1412-1424. 10.1016\/j.cad.2005.02.013.","journal-title":"Comput Aided Des"},{"issue":"5","key":"6189_CR16","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1080\/00268978700102951","volume":"62","author":"K Gibson","year":"1987","unstructured":"Gibson K, Scheraga H: Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii. Molecular Physics. 1987, 62 (5): 1247-1265. 10.1080\/00268978700102951.","journal-title":"Molecular Physics"},{"issue":"5","key":"6189_CR17","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1002\/jcc.540150504","volume":"15","author":"M Petitjean","year":"1994","unstructured":"Petitjean M: On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects. Journal of Computational Chemistry. 1994, 15 (5): 507-523. 10.1002\/jcc.540150504.","journal-title":"Journal of Computational Chemistry"},{"key":"6189_CR18","unstructured":"OpenCL Website. 2012, [\n                    http:\/\/www.khronos.org\/opencl\/\n                    \n                  ]"},{"issue":"3","key":"6189_CR19","doi-asserted-by":"publisher","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 HC: Accelerated Visualization of Dynamic Molecular Surfaces. Comput Graph Forum. 2010, 29 (3): 943-952. 10.1111\/j.1467-8659.2009.01693.x. [\n                    http:\/\/dx.doi.org\/10.1111\/j.1467-8659.2009.01693.x\n                    \n                  ]","journal-title":"Comput Graph Forum"},{"key":"6189_CR20","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1007\/PL00009412","volume":"21","author":"H Edelsbrunner","year":"1999","unstructured":"Edelsbrunner H: Deformable Smooth Surface Design. Discrete Comput Geom. 1999, 21: 87-115. 10.1007\/PL00009412.","journal-title":"Discrete Comput Geom"},{"issue":"5","key":"6189_CR21","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1109\/TVCG.2004.30","volume":"10","author":"G Grigoryan","year":"2004","unstructured":"Grigoryan G, Rheingans P: Point-Based Probabilistic Surfaces to Show Surface Uncertainty. IEEE Transactions on Visualization and Computer Graphics. 2004, 10 (5): 564-573. 10.1109\/TVCG.2004.30. [\n                    http:\/\/dx.doi.org\/10.1109\/TVCG.2004.30\n                    \n                  ]","journal-title":"IEEE Transactions on Visualization and Computer Graphics"},{"issue":"3","key":"6189_CR22","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1111\/j.1467-8659.2011.01942.x","volume":"30","author":"K P\u00f6thkow","year":"2011","unstructured":"P\u00f6thkow K, Weber B, Hege HC: Probabilistic Marching Cubes. Computer Graphics Forum. 2011, 30 (3): 931-940. 10.1111\/j.1467-8659.2011.01942.x. [\n                    http:\/\/www.zib.de\/visual\/publications\/sources\/src-2011\/probabilistic_marching_cubes.pdf\n                    \n                  ]","journal-title":"Computer Graphics Forum"},{"issue":"4","key":"6189_CR23","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1006\/jmbi.1999.3027","volume":"291","author":"H Luecke","year":"1999","unstructured":"Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK: Structure of bacteriorhodopsin at 1.55 \u00c5resolution. J Mol Biol. 1999, 291 (4): 899-911. 10.1006\/jmbi.1999.3027. [\n                    http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0022283699930279\n                    \n                  ]","journal-title":"J Mol Biol"},{"issue":"5","key":"6189_CR24","doi-asserted-by":"publisher","first-page":"3252","DOI":"10.1529\/biophysj.104.047993","volume":"88","author":"S Grudinin","year":"2005","unstructured":"Grudinin S, B\u00fcldt G, Gordeliy V, Baumgaertner A: Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin - Molecular Dynamics Simulations of the Ground State and the M-Intermediate. Biophys J. 2005, 88 (5): 3252-3261. 10.1529\/biophysj.104.047993. [\n                    http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349505733762\n                    \n                  ]","journal-title":"Biophys J"},{"key":"6189_CR25","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/s00232-010-9329-3","volume":"239","author":"AN Bondar","year":"2011","unstructured":"Bondar AN, Fischer S, Smith J: Water Pathways in the Bacteriorhodopsin Proton Pump. J Membr Biol. 2011, 239: 73-84. 10.1007\/s00232-010-9329-3. [10.1007\/s00232-010-9329-3], [\n                    http:\/\/dx.doi.org\/10.1007\/s00232-010-9329-3\n                    \n                  ]","journal-title":"J Membr Biol"},{"issue":"3","key":"6189_CR26","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1111\/j.1467-8659.2011.01916.x","volume":"30","author":"M Krone","year":"2011","unstructured":"Krone M, Falk M, Rehm S, Pleiss J, Ertl T: Interactive Exploration of Protein Cavities. Comput Graph Forum. 2011, 30 (3): 673-682. 10.1111\/j.1467-8659.2011.01916.x.","journal-title":"Comput Graph Forum"},{"key":"6189_CR27","first-page":"333","volume-title":"In: Proceedings of Vision, Modeling and Visualization 2006","author":"J Meyer-Spradow","year":"2006","unstructured":"Meyer-Spradow J, Ropinski T, Vahrenhold J, Hinrichs K: K.H.: Illustrating Dynamics of Time-Varying Volume Datasets in Static Images. In: Proceedings of Vision, Modeling and Visualization 2006. 2006, 333-340."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S19-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T20:26:14Z","timestamp":1548188774000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S19-S5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11]]},"references-count":27,"journal-issue":{"issue":"S19","published-print":{"date-parts":[[2013,11]]}},"alternative-id":["6189"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s19-s5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11]]},"article-number":"S5"}}