{"id":"https://openalex.org/W2160715766","doi":"https://doi.org/10.1109/tvcg.2015.2467434","title":"AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics","display_name":"AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics","publication_year":2015,"publication_date":"2015-08-14","ids":{"openalex":"https://openalex.org/W2160715766","doi":"https://doi.org/10.1109/tvcg.2015.2467434","mag":"2160715766","pmid":"https://pubmed.ncbi.nlm.nih.gov/26529726"},"language":"en","primary_location":{"id":"doi:10.1109/tvcg.2015.2467434","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2015.2467434","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5039343836","display_name":"Jan By\u0161ka","orcid":"https://orcid.org/0000-0001-9483-7562"},"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":"Jan Byska","raw_affiliation_strings":["Masaryk University, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016122563","display_name":"Mathieu Le Muzic","orcid":null},"institutions":[{"id":"https://openalex.org/I145847075","display_name":"TU Wien","ror":"https://ror.org/04d836q62","country_code":"AT","type":"education","lineage":["https://openalex.org/I145847075"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Mathieu Le Muzic","raw_affiliation_strings":["TU Wien, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Wien, Austria","institution_ids":["https://openalex.org/I145847075"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109928029","display_name":"M. Eduard Gr\u00f6ller","orcid":null},"institutions":[{"id":"https://openalex.org/I145847075","display_name":"TU Wien","ror":"https://ror.org/04d836q62","country_code":"AT","type":"education","lineage":["https://openalex.org/I145847075"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["AT","NO"],"is_corresponding":false,"raw_author_name":"M. Eduard Groller","raw_affiliation_strings":["TU Wien, Austria","University of Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Wien, Austria","institution_ids":["https://openalex.org/I145847075"]},{"raw_affiliation_string":"University of Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022294742","display_name":"Ivan Viola","orcid":"https://orcid.org/0000-0003-4248-6574"},"institutions":[{"id":"https://openalex.org/I145847075","display_name":"TU Wien","ror":"https://ror.org/04d836q62","country_code":"AT","type":"education","lineage":["https://openalex.org/I145847075"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["AT","NO"],"is_corresponding":false,"raw_author_name":"Ivan Viola","raw_affiliation_strings":["TU Wien, Austria","University of Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Wien, Austria","institution_ids":["https://openalex.org/I145847075"]},{"raw_affiliation_string":"University of Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"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/I145847075","display_name":"TU Wien","ror":"https://ror.org/04d836q62","country_code":"AT","type":"education","lineage":["https://openalex.org/I145847075"]},{"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":["AT","CZ"],"is_corresponding":false,"raw_author_name":"Barbora Kozlikova","raw_affiliation_strings":["Masaryk University, Czech Republic","TU Wien, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"TU Wien, Austria","institution_ids":["https://openalex.org/I145847075"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.1824,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.78683496,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"22","issue":"1","first_page":"747","last_page":"756"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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":0.9983000159263611,"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/T10799","display_name":"Data Visualization and Analytics","score":0.9869999885559082,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9448000192642212,"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/computer-science","display_name":"Computer science","score":0.6910021305084229},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6629993319511414},{"id":"https://openalex.org/keywords/curvature","display_name":"Curvature","score":0.6567260026931763},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5854231119155884},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5537374019622803},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5119398832321167},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5111415982246399},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46238890290260315},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3295973539352417},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3221226930618286},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.22403672337532043},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17384907603263855},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14039099216461182},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09182050824165344},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08505088090896606}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6910021305084229},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6629993319511414},{"id":"https://openalex.org/C195065555","wikidata":"https://www.wikidata.org/wiki/Q214881","display_name":"Curvature","level":2,"score":0.6567260026931763},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5854231119155884},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5537374019622803},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5119398832321167},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5111415982246399},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46238890290260315},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3295973539352417},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3221226930618286},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.22403672337532043},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17384907603263855},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14039099216461182},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09182050824165344},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08505088090896606},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tvcg.2015.2467434","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2015.2467434","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},{"id":"pmid:26529726","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26529726","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on visualization and computer graphics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G8424453579","display_name":"Visual Computing: Illustrative Visualization","funder_award_id":"VRG11-010","funder_id":"https://openalex.org/F4320321003","funder_display_name":"Vienna Science and Technology Fund"}],"funders":[{"id":"https://openalex.org/F4320321003","display_name":"Vienna Science and Technology Fund","ror":"https://ror.org/01f9mc681"},{"id":"https://openalex.org/F4320323163","display_name":"OeAD-GmbH","ror":"https://ror.org/05y9csv14"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1879416943","https://openalex.org/W1974635207","https://openalex.org/W1993623134","https://openalex.org/W2034526679","https://openalex.org/W2039181331","https://openalex.org/W2065371116","https://openalex.org/W2065894452","https://openalex.org/W2111736285","https://openalex.org/W2111967893","https://openalex.org/W2126152274","https://openalex.org/W2128934301","https://openalex.org/W2131080603","https://openalex.org/W2135711052","https://openalex.org/W2137825366","https://openalex.org/W2138992251","https://openalex.org/W2140387095","https://openalex.org/W2141069751","https://openalex.org/W2141891891","https://openalex.org/W2144742694","https://openalex.org/W2145247721","https://openalex.org/W2152167878","https://openalex.org/W2155758860","https://openalex.org/W2171750292","https://openalex.org/W2234920829","https://openalex.org/W3146761106","https://openalex.org/W4251304284","https://openalex.org/W4252100329","https://openalex.org/W6689435558"],"related_works":["https://openalex.org/W2193237397","https://openalex.org/W55883722","https://openalex.org/W2084679820","https://openalex.org/W2391644650","https://openalex.org/W2387003094","https://openalex.org/W2394379345","https://openalex.org/W2079726820","https://openalex.org/W3215763795","https://openalex.org/W4288816678","https://openalex.org/W2150659537"],"abstract_inverted_index":{"In":[0,114],"this":[1,115],"paper":[2],"we":[3,23],"propose":[4],"a":[5,48,60,100,123,174,195],"novel":[6],"method":[7,84],"for":[8,166],"the":[9,27,30,64,86,110,129,135,139,146,158,162,170],"interactive":[10],"exploration":[11],"of":[12,18,63,103,125,134,148],"protein":[13,171],"tunnels.":[14],"The":[15,83,94,177],"basic":[16],"principle":[17],"our":[19],"approach":[20],"is":[21,33,44,96,120,189],"that":[22],"entirely":[24],"abstract":[25],"from":[26],"3D/4D":[28],"space":[29],"simulated":[31],"phenomenon":[32],"embedded":[34],"in.":[35],"A":[36],"complex":[37],"3D":[38],"structure":[39],"and":[40,52,67,75,90,131,194],"its":[41,53,91],"curvature":[42],"information":[43],"represented":[45,78,121],"only":[46],"by":[47,79,122,191],"straightened":[49],"tunnel":[50,88,111],"centerline":[51],"width":[54],"profile.":[55],"This":[56,142],"representation":[57,143],"focuses":[58],"on":[59,138],"key":[61,73],"aspect":[62],"studied":[65],"geometry":[66],"frees":[68],"up":[69],"graphical":[70],"estate":[71],"to":[72,153,160],"chemical":[74],"physical":[76],"properties":[77],"surrounding":[80],"amino":[81,105,118,136,149,164],"acids.":[82],"shows":[85,145],"detailed":[87],"profile":[89,95],"temporal":[92,132],"aggregation.":[93],"interactively":[97],"linked":[98],"with":[99,151,184],"visual":[101],"overview":[102],"all":[104],"acids":[106,150,165],"which":[107,168,198],"are":[108,199],"lining":[109],"over":[112],"time.":[113],"overview,":[116],"each":[117],"acid":[119,137],"set":[124],"colored":[126],"lines":[127],"depicting":[128],"spatial":[130],"impact":[133],"corresponding":[140],"tunnel.":[141],"clearly":[144],"importance":[147],"respect":[152],"selected":[154],"criteria.":[155],"It":[156],"helps":[157],"biochemists":[159],"select":[161],"candidate":[163],"mutation":[167],"changes":[169],"function":[172],"in":[173,181],"desired":[175],"way.":[176],"AnimoAminoMiner":[178],"was":[179],"designed":[180],"close":[182],"cooperation":[183],"domain":[185],"experts.":[186],"Its":[187],"usefulness":[188],"documented":[190],"their":[192],"feedback":[193],"case":[196],"study,":[197],"included.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
