{"id":"https://openalex.org/W2527381117","doi":"https://doi.org/10.1109/mmar.2016.7575276","title":"Application of sampling-based path planning for tunnel detection in dynamic protein structures","display_name":"Application of sampling-based path planning for tunnel detection in dynamic protein structures","publication_year":2016,"publication_date":"2016-08-01","ids":{"openalex":"https://openalex.org/W2527381117","doi":"https://doi.org/10.1109/mmar.2016.7575276","mag":"2527381117"},"language":"en","primary_location":{"id":"doi:10.1109/mmar.2016.7575276","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mmar.2016.7575276","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 21st International Conference on Methods and Models in Automation and Robotics (MMAR)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083101752","display_name":"Vojt\u011bch Von\u00e1sek","orcid":"https://orcid.org/0000-0001-9224-2151"},"institutions":[{"id":"https://openalex.org/I44504214","display_name":"Czech Technical University in Prague","ror":"https://ror.org/03kqpb082","country_code":"CZ","type":"education","lineage":["https://openalex.org/I44504214"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Vojtech Vonasek","raw_affiliation_strings":["Faculty of Electrical Engineering, Czech Technical University in Prague, Prague 6, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Electrical Engineering, Czech Technical University in Prague, Prague 6, Czech Republic","institution_ids":["https://openalex.org/I44504214"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022022242","display_name":"Barbora Kozl\u00edkov\u00e1","orcid":"https://orcid.org/0000-0003-0045-0872"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Barbora Kozlikova","raw_affiliation_strings":["Faculty of Informatics, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Informatics, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083101752"],"corresponding_institution_ids":["https://openalex.org/I44504214"],"apc_list":null,"apc_paid":null,"fwci":0.6669,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.73732867,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1010","last_page":"1015"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9882000088691711,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9732000231742859,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/voronoi-diagram","display_name":"Voronoi diagram","score":0.8143938183784485},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6104047298431396},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.561398446559906},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5577107667922974},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"Protein dynamics","score":0.5440593957901001},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.46592211723327637},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4545329213142395},{"id":"https://openalex.org/keywords/random-tree","display_name":"Random tree","score":0.4538690745830536},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.4326452612876892},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41494977474212646},{"id":"https://openalex.org/keywords/space-partitioning","display_name":"Space partitioning","score":0.4148481488227844},{"id":"https://openalex.org/keywords/motion-planning","display_name":"Motion planning","score":0.37841176986694336},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.35724228620529175},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22504550218582153},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17790332436561584},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.14479681849479675},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12944933772087097},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.10424420237541199},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0912940502166748}],"concepts":[{"id":"https://openalex.org/C24881265","wikidata":"https://www.wikidata.org/wiki/Q757267","display_name":"Voronoi diagram","level":2,"score":0.8143938183784485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6104047298431396},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.561398446559906},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5577107667922974},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.5440593957901001},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.46592211723327637},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4545329213142395},{"id":"https://openalex.org/C2776839635","wikidata":"https://www.wikidata.org/wiki/Q14942679","display_name":"Random tree","level":4,"score":0.4538690745830536},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.4326452612876892},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41494977474212646},{"id":"https://openalex.org/C13670688","wikidata":"https://www.wikidata.org/wiki/Q3500548","display_name":"Space partitioning","level":2,"score":0.4148481488227844},{"id":"https://openalex.org/C81074085","wikidata":"https://www.wikidata.org/wiki/Q366872","display_name":"Motion planning","level":3,"score":0.37841176986694336},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35724228620529175},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22504550218582153},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17790332436561584},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.14479681849479675},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12944933772087097},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.10424420237541199},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0912940502166748},{"id":"https://openalex.org/C90509273","wikidata":"https://www.wikidata.org/wiki/Q11012","display_name":"Robot","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/mmar.2016.7575276","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mmar.2016.7575276","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 21st International Conference on Methods and Models in Automation and Robotics (MMAR)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W131069610","https://openalex.org/W1974635207","https://openalex.org/W2001008407","https://openalex.org/W2039181331","https://openalex.org/W2051757997","https://openalex.org/W2055201760","https://openalex.org/W2081498635","https://openalex.org/W2131080603","https://openalex.org/W2137825366","https://openalex.org/W2138992251","https://openalex.org/W2140387095","https://openalex.org/W2155758860","https://openalex.org/W2220469999","https://openalex.org/W6605295560"],"related_works":["https://openalex.org/W1991478428","https://openalex.org/W1987694097","https://openalex.org/W3158818664","https://openalex.org/W2797949337","https://openalex.org/W2863424594","https://openalex.org/W2372633663","https://openalex.org/W4388720133","https://openalex.org/W2564325388","https://openalex.org/W2108906364","https://openalex.org/W2371294653"],"abstract_inverted_index":{"Behavior":[0],"and":[1,38,95],"properties":[2,48],"of":[3,74,89,129,134,152],"proteins":[4,111],"as":[5,7,17],"well":[6],"other":[8],"bio-macromolecules":[9],"is":[10,69,92,146],"influenced":[11],"by":[12,71],"internal":[13],"void":[14],"space":[15,128],"such":[16],"tunnels":[18,37],"or":[19,51],"cavities.":[20],"Tunnels":[21,56],"are":[22,137],"paths":[23],"leading":[24],"from":[25],"an":[26,44],"active":[27],"site":[28],"inside":[29],"the":[30,130,135,153],"protein":[31,47,66,75,141,160],"to":[32,53,84,140,148],"its":[33],"surface.":[34],"Knowledge":[35],"about":[36],"their":[39],"evolution":[40],"in":[41,80,109],"time":[42,94],"provides":[43],"insight":[45],"into":[46],"(e.g.":[49],"stability":[50],"resistance":[52],"a":[54,72,103,122],"co-solvent).":[55],"can":[57],"be":[58,85],"found":[59],"using":[60],"Voronoi":[61],"diagrams":[62],"(VD).":[63],"To":[64],"consider":[65],"dynamics,":[67],"that":[68],"represented":[70],"sequence":[73],"snapshots,":[76],"correspondences":[77,91],"between":[78],"VD":[79],"these":[81,90],"snapshots":[82],"need":[83],"found.":[86],"The":[87,119,132,143],"computation":[88],"however":[93],"memory":[96],"consuming.":[97],"In":[98],"this":[99],"paper,":[100],"we":[101],"propose":[102],"novel":[104],"method":[105,120],"for":[106,159],"tunnel":[107],"detection":[108],"dynamic":[110],"based":[112],"on":[113],"Rapidly":[114],"Exploring":[115],"Random":[116],"Tree":[117],"(RRT).":[118],"builds":[121],"single":[123],"configuration":[124],"tree":[125,136],"describing":[126],"free":[127],"protein.":[131],"nodes":[133],"pruned":[138],"according":[139],"dynamics.":[142],"proposed":[144],"approach":[145],"compared":[147],"CAVER":[149],"3.0,":[150],"one":[151],"widely":[154],"used":[155],"freely":[156],"available":[157],"tools":[158],"analysis.":[161]},"counts_by_year":[{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
