{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T13:05:58Z","timestamp":1773666358686,"version":"3.50.1"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1913-4","type":"journal-article","created":{"date-parts":[[2017,11,16]],"date-time":"2017-11-16T08:09:06Z","timestamp":1510819746000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["GPU-based detection of protein cavities using Gaussian surfaces"],"prefix":"10.1186","volume":"18","author":[{"given":"S\u00e9rgio E. D.","family":"Dias","sequence":"first","affiliation":[]},{"given":"Ana Mafalda","family":"Martins","sequence":"additional","affiliation":[]},{"given":"Quoc T.","family":"Nguyen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5804-5717","authenticated-orcid":false,"given":"Abel J. P.","family":"Gomes","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,11,16]]},"reference":[{"issue":"2","key":"1913_CR1","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1002\/prot.21283","volume":"68","author":"T Kawabata","year":"2007","unstructured":"Kawabata T, Go N. Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites. Protein Struct Funct Bioinforma. 2007; 68(2):516\u201329.","journal-title":"Protein Struct Funct Bioinforma"},{"issue":"11","key":"1913_CR2","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1021\/ci100241y","volume":"50","author":"A Volkamer","year":"2010","unstructured":"Volkamer A, Griewel A, Grombacher T, Rarey M. Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. J Chem Inf Model. 2010; 50(11):2041\u201352.","journal-title":"J Chem Inf Model"},{"issue":"3","key":"1913_CR3","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1111\/cgf.12928","volume":"35","author":"M Krone","year":"2016","unstructured":"Krone M, Kozl\u00edkov\u00e1 B, Lindow N, Baaden M, Baum D, Parulek J, Hege HC, Viola I. Visual Analysis of Biomolecular Cavities: State of the Art. Comput Graph Forum. 2016; 35(3):527\u201351.","journal-title":"Comput Graph Forum"},{"key":"1913_CR4","doi-asserted-by":"crossref","unstructured":"Sim\u00f5es T, Lopes D, Dias S, Fernandes F, Pereira J, Jorge J, Bajaj C, Gomes A. Geometric detection algorithms for cavities on protein surfaces in molecular graphics: a survey. Comput Graph Forum. 2017. doi:\n                        10.1111\/cgf.13158\n                        \n                    .","DOI":"10.1111\/cgf.13158"},{"issue":"4","key":"1913_CR5","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/0263-7855(89)80010-4","volume":"7","author":"R Voorintholt","year":"1989","unstructured":"Voorintholt R, Kosters MT, Vegter G, Vriend G, Hol WG. A very fast program for visualizing protein surfaces, channels and cavities. J Mol Graph. 1989; 7(4):243\u20135.","journal-title":"J Mol Graph"},{"key":"1913_CR6","volume-title":"Proceedings of the Computational Systems and Bioinformatics Conference (CSB\u20192007)","author":"X Zhang","year":"2007","unstructured":"Zhang X, Bajaj C. Extraction, quantification and visualization of protein pockets. In: Proceedings of the Computational Systems and Bioinformatics Conference (CSB\u20192007). California: Life Sciences Society: 2007. p. 275\u201386."},{"issue":"4","key":"1913_CR7","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/0263-7855(92)80074-N","volume":"10","author":"DG Levitt","year":"1992","unstructured":"Levitt DG, Banaszak LJ. POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph. 1992; 10(4):229\u201334.","journal-title":"J Mol Graph"},{"issue":"3","key":"1913_CR8","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1111\/cgf.12120","volume":"32","author":"M Krone","year":"2013","unstructured":"Krone M, Reina G, Schulz C, Kulschewski T, Pleiss J, Ertl T. Interactive extraction and tracking of biomolecular surface features. Comput Graph Forum. 2013; 32(3):331\u201340.","journal-title":"Comput Graph Forum"},{"issue":"1","key":"1913_CR9","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.jsb.2007.09.005","volume":"161","author":"Y Kalidas","year":"2008","unstructured":"Kalidas Y, Chandra N. PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins. J Struct Biol. 2008; 161(1):31\u201342.","journal-title":"J Struct Biol"},{"issue":"1","key":"1913_CR10","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1186\/1471-2105-15-197","volume":"15","author":"SH Oliveira","year":"2014","unstructured":"Oliveira SH, Ferraz FA, Honorato RV, Xavier-Neto J, Sobreira TJ, de Oliveira PS. KVFinder: steered identification of protein cavities as a PyMOL plugin. BMC Bioinformatics. 2014; 15(1):197.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"1913_CR11","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1093\/bioinformatics\/btq672","volume":"27","author":"H Zhu","year":"2011","unstructured":"Zhu H, Pisabarro MT. MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets. Bioinformatics. 2011; 27(3):351\u20138.","journal-title":"Bioinformatics"},{"key":"1913_CR12","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/j.future.2016.07.009","volume":"67","author":"SED Dias","year":"2017","unstructured":"Dias SED, Nguyen QT, Jorge JA, Gomes AJP. Multi-GPU-based detection of protein cavities using critical points. Futur Gener Comput Syst. 2017; 67:430\u201340.","journal-title":"Futur Gener Comput Syst"},{"key":"1913_CR13","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-84882-406-5","volume-title":"Implicit Curves and Surfaces: Mathematics, Data Structures, and Algorithms","author":"A Gomes","year":"2009","unstructured":"Gomes A, Voiculescu I, Jorge J, Wyvill B, Galbraith C. Implicit Curves and Surfaces: Mathematics, Data Structures, and Algorithms. London: Springer; 2009."},{"issue":"4","key":"1913_CR14","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1002\/prot.20897","volume":"63","author":"M Nayal","year":"2006","unstructured":"Nayal M, Honig B. On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites. Proteins. 2006; 63(4):892\u2013906.","journal-title":"Proteins"},{"issue":"1","key":"1913_CR15","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/0263-7855(86)80086-8","volume":"4","author":"M Connolly","year":"1986","unstructured":"Connolly M. Measurement of protein surface shape by solid angles. J Mol Graph. 1986; 4(1):3\u20136.","journal-title":"J Mol Graph"},{"issue":"6","key":"1913_CR16","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1016\/j.cagd.2006.02.003","volume":"23","author":"V Natarajan","year":"2006","unstructured":"Natarajan V, Wang Y, Bremer PT, Pascucci V, Hamann B. Segmenting molecular surfaces. Comput Aided Geom Des. 2006; 23(6):495\u2013509.","journal-title":"Comput Aided Geom Des"},{"issue":"1","key":"1913_CR17","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/jcc.540130110","volume":"13","author":"CD Zachmann","year":"1992","unstructured":"Zachmann CD, Heiden W, Schlenkrich M, Brickmann J. Topological analysis of complex molecular surfaces. J Comput Chem. 1992; 13(1):76\u201384.","journal-title":"J Comput Chem"},{"key":"1913_CR18","volume-title":"Proceedings of the 2012 IEEE Symposium on Biological Data Visualization (BioVis\u20192012)","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. In: Proceedings of the 2012 IEEE Symposium on Biological Data Visualization (BioVis\u20192012). Washington: IEEE Press: 2012. p. 115\u201322."},{"issue":"1","key":"1913_CR19","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1146\/annurev.bb.06.060177.001055","volume":"6","author":"FM Richards","year":"1977","unstructured":"Richards FM. Areas, volumes, packing, and protein structure. Annu Rev Biophys Bioeng. 1977; 6(1):151\u201376.","journal-title":"Annu Rev Biophys Bioeng"},{"issue":"11","key":"1913_CR20","doi-asserted-by":"crossref","first-page":"3503","DOI":"10.1021\/j100011a016","volume":"99","author":"JA Grant","year":"1995","unstructured":"Grant JA, Pickup BT. A Gaussian description of molecular shape. J Phys Chem. 1995; 99(11):3503\u201310.","journal-title":"J Phys Chem"},{"issue":"1\u20133","key":"1913_CR21","first-page":"17","volume":"19","author":"D Borland","year":"2011","unstructured":"Borland D. Ambient occlusion opacity mapping for visualization of internal molecular structure. J WSCG. 2011; 19(1\u20133):17\u201324.","journal-title":"J WSCG"},{"issue":"12","key":"1913_CR22","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/S0968-0004(97)01140-7","volume":"22","author":"RA Laskowski","year":"1997","unstructured":"Laskowski RA, Hutchinson GE, Michie AD, Wallace AC, Jones ML, Thornton JM. PDBsum: a web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci. 1997; 22(12):488\u201390.","journal-title":"Trends Biochem Sci"},{"key":"1913_CR23","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1093\/nar\/gkq395","volume":"38","author":"NR Voss","year":"2010","unstructured":"Voss NR, Gerstein M. 3v: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res. 2010; 38:555.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"1913_CR24","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1145\/357306.357310","volume":"1","author":"JF Blinn","year":"1982","unstructured":"Blinn JF. A generalization of algebraic surface drawing. ACM Trans Graph. 1982; 1(3):235\u201356.","journal-title":"ACM Trans Graph"},{"issue":"3","key":"1913_CR25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0051307","volume":"8","author":"R Chowdhury","year":"2013","unstructured":"Chowdhury R, Rasheed M, Keidel D, Moussalem M, Olson A, Sanner M, Bajaj C. Protein-protein docking with f2dock 2.0 and gb-rerank. PLoS ONE. 2013; 8(3):1\u201319.","journal-title":"PLoS ONE"},{"issue":"6","key":"1913_CR26","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/S0263-7855(97)00008-8","volume":"14","author":"RR Gabdoulline","year":"1996","unstructured":"Gabdoulline RR, Wade RC. Analytically defined surfaces to analyze molecular interaction properties. J Mol Graph. 1996; 14(6):341\u201353.","journal-title":"J Mol Graph"},{"issue":"6","key":"1913_CR27","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/j.cagd.2006.01.008","volume":"23","author":"Y Zhang","year":"2006","unstructured":"Zhang Y, Xu G, Bajaj C. Quality meshing of implicit solvation models of biomolecular structures. Comput Aided Geom Des. 2006; 23(6):510\u201330.","journal-title":"Comput Aided Geom Des"},{"issue":"1","key":"1913_CR28","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1109\/TCBB.2009.57","volume":"8","author":"CL Bajaj","year":"2011","unstructured":"Bajaj CL, Chowdhury R, Siddahanavalli V. f\n                    2dock: Fast fourier protein-protein docking. IEEE\/ACM Trans Comput Biol Bioinforma. 2011; 8(1):45\u201358.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma"},{"key":"1913_CR29","volume-title":"CUDA Programming: A Developer\u2019s Guide to Parallel Computing with GPUs","author":"S Cook","year":"2012","unstructured":"Cook S. CUDA Programming: A Developer\u2019s Guide to Parallel Computing with GPUs, Applications of GPU Computing. San Francisco: Morgan Kaufmann; 2012."},{"key":"1913_CR30","volume-title":"Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD\u201996), Portland, Oregon, USA, August 2-4","author":"M Ester","year":"1996","unstructured":"Ester M, Kriegel HP, Sander J, Xu X. A density-based algorithm for discovering clusters a density-based algorithm for discovering clusters in large spatial databases with noise. In: Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD\u201996), Portland, Oregon, USA, August 2-4. Palo Alto: AAAI Press: 1996. p. 226\u201331."},{"key":"1913_CR31","volume-title":"Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing","author":"S Dias","year":"2010","unstructured":"Dias S, Bora K, Gomes A. CUDA-based triangulations of convolution molecular surfaces. In: Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing. HPDC \u201910. New York: ACM: 2010. p. 531\u201340."},{"issue":"17","key":"1913_CR32","doi-asserted-by":"crossref","first-page":"2280","DOI":"10.1002\/cpe.1783","volume":"23","author":"S Dias","year":"2011","unstructured":"Dias S, Gomes A. Graphics processing unit- based triangulations of Blinn molecular surfaces. Concurr Comput Pract Experience. 2011; 23(17):2280\u201391.","journal-title":"Concurr Comput Pract Experience"},{"key":"1913_CR33","unstructured":"Dias S, Gomes AJP. Computational Electrostatics for Biological Applications In: Rocchia W, Spagnuolo M, editors. Cham: Springer: 2015. p. 177\u201398."},{"key":"1913_CR34","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.parco.2014.09.009","volume":"42","author":"SED Dias","year":"2015","unstructured":"Dias SED, Gomes AJP. Triangulating molecular surfaces over a LAN of GPU-enabled computers. Parallel Comput. 2015; 42:35\u201347.","journal-title":"Parallel Comput"},{"key":"1913_CR35","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1093\/nar\/gkm839","volume":"36","author":"BH Dessailly","year":"2008","unstructured":"Dessailly BH, Lensink MF, Wodak SJ. LigASite: a database of biologically relevant binding sites in proteins with known apo-structures. Acid Nucleic Res. 2008; 36:667\u201373.","journal-title":"Acid Nucleic Res"},{"issue":"1","key":"1913_CR36","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1093\/bioinformatics\/btp599","volume":"26","author":"J Yu","year":"2010","unstructured":"Yu J, Zhou Y, Tanaka I, Yao M. Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics. 2010; 26(1):46\u201352.","journal-title":"Bioinformatics"},{"issue":"5","key":"1913_CR37","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/0263-7855(95)00073-9","volume":"13","author":"RA Laskowski","year":"1995","unstructured":"Laskowski RA. SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph. 1995; 13(5):323\u201330.","journal-title":"J Mol Graph"},{"issue":"4","key":"1913_CR38","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1023\/A:1008124202956","volume":"14","author":"J Brady","year":"2000","unstructured":"Brady J, Patrick G, Stouten PW. Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des. 2000; 14(4):383\u2013401.","journal-title":"J Comput Aided Mol Des"},{"issue":"1","key":"1913_CR39","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1471-2105-10-168","volume":"10","author":"V Le Guilloux","year":"2009","unstructured":"Le Guilloux V, Schmidtke P, Tuffery P. Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics. 2009; 10(1):168.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"1913_CR40","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1002\/prot.22639","volume":"78","author":"T Kawabata","year":"2010","unstructured":"Kawabata T. Detection of multiscale pockets on protein surfaces using mathematical morphology. Proteins. 2010; 78(5):1195\u2013211.","journal-title":"Proteins"},{"issue":"12","key":"1913_CR41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1000585","volume":"5","author":"JA Capra","year":"2009","unstructured":"Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3d structure. PLOS Comput Biol. 2009; 5(12):1\u201318.","journal-title":"PLOS Comput Biol"},{"issue":"4","key":"1913_CR42","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1089\/omi.2009.0045","volume":"13","author":"B Huang","year":"2009","unstructured":"Huang B. MetaPocket: A meta approach to improve protein ligand binding site prediction. OMICS. 2009; 13(4):325\u201330.","journal-title":"OMICS"},{"issue":"5","key":"1913_CR43","doi-asserted-by":"crossref","first-page":"2151","DOI":"10.1021\/ct401098b","volume":"10","author":"T Paramo","year":"2014","unstructured":"Paramo T, East A, Garz\u00f3n D, Ulmschneider MB, Bond PJ. Efficient characterization of protein cavities within molecular simulation trajectories: trj_cavity. J Chem Theory Comput. 2014; 10(5):2151\u201364.","journal-title":"J Chem Theory Comput"},{"issue":"15-16","key":"1913_CR44","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1016\/j.drudis.2010.05.015","volume":"15","author":"S P\u00e9rot","year":"2010","unstructured":"P\u00e9rot S, Sperandio O, Miteva MA, Camproux AC, Villoutreix BO. Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov Today. 2010; 15(15-16):656\u201367.","journal-title":"Drug Discov Today"},{"issue":"6","key":"1913_CR45","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1074\/mcp.M400159-MCP200","volume":"4","author":"J An","year":"2005","unstructured":"An J, Totrov M, Abagyan R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteome. 2005; 4(6):752\u201361.","journal-title":"Mol Cell Proteome"},{"key":"1913_CR46","volume-title":"Practical Handbook of Curve Fitting","author":"S Arlinghaus","year":"1994","unstructured":"Arlinghaus S. Practical Handbook of Curve Fitting. Boca Raton: CRC Press; 1994."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1913-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,11,16]],"date-time":"2017-11-16T08:09:55Z","timestamp":1510819795000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1913-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,16]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1913"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1913-4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,16]]},"article-number":"493"}}