{"id":"https://openalex.org/W2027095034","doi":"https://doi.org/10.1109/idaacs.2011.6072742","title":"Integrated tools for molecular dynamics simulation data analysis in the MolDynGrid virtual laboratory","display_name":"Integrated tools for molecular dynamics simulation data analysis in the MolDynGrid virtual laboratory","publication_year":2011,"publication_date":"2011-09-01","ids":{"openalex":"https://openalex.org/W2027095034","doi":"https://doi.org/10.1109/idaacs.2011.6072742","mag":"2027095034"},"language":"en","primary_location":{"id":"doi:10.1109/idaacs.2011.6072742","is_oa":false,"landing_page_url":"https://doi.org/10.1109/idaacs.2011.6072742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 6th IEEE International Conference on Intelligent Data Acquisition and Advanced Computing Systems","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/A5024052239","display_name":"Oleksandr V. Savytskyi","orcid":"https://orcid.org/0000-0002-8150-4416"},"institutions":[{"id":"https://openalex.org/I149851306","display_name":"National Academy of Sciences of Ukraine","ror":"https://ror.org/00je4t102","country_code":"UA","type":"funder","lineage":["https://openalex.org/I149851306"]},{"id":"https://openalex.org/I68243183","display_name":"Institute of Molecular Biology and Genetics","ror":"https://ror.org/01rqyr540","country_code":"UA","type":"government","lineage":["https://openalex.org/I149851306","https://openalex.org/I68243183"]}],"countries":["UA"],"is_corresponding":true,"raw_author_name":"O. V. Savytskyi","raw_affiliation_strings":["Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine","Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Akademika Zabolotnogo Str., 150; Kyiv-03680; Ukraine"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine","institution_ids":["https://openalex.org/I68243183","https://openalex.org/I149851306"]},{"raw_affiliation_string":"Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Akademika Zabolotnogo Str., 150; Kyiv-03680; Ukraine","institution_ids":["https://openalex.org/I149851306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053513242","display_name":"Ievgen Sliusar","orcid":"https://orcid.org/0000-0002-1905-3810"},"institutions":[{"id":"https://openalex.org/I189238007","display_name":"Taras Shevchenko National University of Kyiv","ror":"https://ror.org/02aaqv166","country_code":"UA","type":"education","lineage":["https://openalex.org/I189238007"]}],"countries":["UA"],"is_corresponding":false,"raw_author_name":"I. A. Sliusar","raw_affiliation_strings":["Information and Computer Centre, National Taras Shevchenko University of Kyiv, Kyiv, Ukraine","Information and Computer Centre, National Taras Shevchenko University of Kyiv, Glushkova prosp., 4D, Kyiv, Ukraine"],"affiliations":[{"raw_affiliation_string":"Information and Computer Centre, National Taras Shevchenko University of Kyiv, Kyiv, Ukraine","institution_ids":["https://openalex.org/I189238007"]},{"raw_affiliation_string":"Information and Computer Centre, National Taras Shevchenko University of Kyiv, Glushkova prosp., 4D, Kyiv, Ukraine","institution_ids":["https://openalex.org/I189238007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107463400","display_name":"Semen Yesylevskyy","orcid":"https://orcid.org/0000-0002-6748-8931"},"institutions":[{"id":"https://openalex.org/I75705878","display_name":"Institute of Physics","ror":"https://ror.org/02we6hx96","country_code":"UA","type":"facility","lineage":["https://openalex.org/I149851306","https://openalex.org/I75705878"]},{"id":"https://openalex.org/I149851306","display_name":"National Academy of Sciences of Ukraine","ror":"https://ror.org/00je4t102","country_code":"UA","type":"funder","lineage":["https://openalex.org/I149851306"]}],"countries":["UA"],"is_corresponding":false,"raw_author_name":"S. O. Yesylevskyy","raw_affiliation_strings":["Institute of Physics, National Academy of Sciences of Ukraine, Kyiv, Ukraine","Institute of Physics; National Academy of Sciences of Ukraine; Prospect Nauki, 46; Kyiv-03039; Ukraine"],"affiliations":[{"raw_affiliation_string":"Institute of Physics, National Academy of Sciences of Ukraine, Kyiv, Ukraine","institution_ids":["https://openalex.org/I75705878","https://openalex.org/I149851306"]},{"raw_affiliation_string":"Institute of Physics; National Academy of Sciences of Ukraine; Prospect Nauki, 46; Kyiv-03039; Ukraine","institution_ids":["https://openalex.org/I149851306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005082546","display_name":"Sergii Stirenko","orcid":"https://orcid.org/0000-0001-5478-0450"},"institutions":[{"id":"https://openalex.org/I70764802","display_name":"National Polytechnic School","ror":"https://ror.org/01gb99w41","country_code":"EC","type":"education","lineage":["https://openalex.org/I70764802"]},{"id":"https://openalex.org/I202483615","display_name":"National Technical University of Ukraine \u201cIgor Sikorsky Kyiv Polytechnic Institute\u201d","ror":"https://ror.org/00syn5v21","country_code":"UA","type":"education","lineage":["https://openalex.org/I202483615"]}],"countries":["EC","UA"],"is_corresponding":false,"raw_author_name":"S. G. Stirenko","raw_affiliation_strings":["High-Performance Computing Center, National Technical University of Ukraine, Kyiv Polytechnic Institute, Kyiv, Ukraine","High-Performance Computing Center, National Technical University of Ukraine \u201cKyiv Polytechnic Institute\u201d, Prospect Peremohy, 37, 03056, Kyiv-56, Ukraine"],"affiliations":[{"raw_affiliation_string":"High-Performance Computing Center, National Technical University of Ukraine, Kyiv Polytechnic Institute, Kyiv, Ukraine","institution_ids":["https://openalex.org/I202483615"]},{"raw_affiliation_string":"High-Performance Computing Center, National Technical University of Ukraine \u201cKyiv Polytechnic Institute\u201d, Prospect Peremohy, 37, 03056, Kyiv-56, Ukraine","institution_ids":["https://openalex.org/I70764802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023962385","display_name":"A. I. Kornelyuk","orcid":"https://orcid.org/0000-0003-0146-2832"},"institutions":[{"id":"https://openalex.org/I68243183","display_name":"Institute of Molecular Biology and Genetics","ror":"https://ror.org/01rqyr540","country_code":"UA","type":"government","lineage":["https://openalex.org/I149851306","https://openalex.org/I68243183"]},{"id":"https://openalex.org/I149851306","display_name":"National Academy of Sciences of Ukraine","ror":"https://ror.org/00je4t102","country_code":"UA","type":"funder","lineage":["https://openalex.org/I149851306"]}],"countries":["UA"],"is_corresponding":false,"raw_author_name":"A. I. Kornelyuk","raw_affiliation_strings":["Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine","Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Akademika Zabolotnogo Str., 150; Kyiv-03680; Ukraine"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine","institution_ids":["https://openalex.org/I68243183","https://openalex.org/I149851306"]},{"raw_affiliation_string":"Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Akademika Zabolotnogo Str., 150; Kyiv-03680; Ukraine","institution_ids":["https://openalex.org/I149851306"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5024052239"],"corresponding_institution_ids":["https://openalex.org/I149851306","https://openalex.org/I68243183"],"apc_list":null,"apc_paid":null,"fwci":1.0612,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.77791742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"9","issue":null,"first_page":"208","last_page":"211"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9884999990463257,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9884999990463257,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9089000225067139,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8093067407608032},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7259921431541443},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.6929019689559937},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6274981498718262},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5369664430618286},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4720920920372009},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.45235779881477356},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.45075199007987976},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2893838584423065},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.08010914921760559}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8093067407608032},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7259921431541443},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.6929019689559937},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6274981498718262},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5369664430618286},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4720920920372009},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.45235779881477356},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.45075199007987976},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2893838584423065},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.08010914921760559},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/idaacs.2011.6072742","is_oa":false,"landing_page_url":"https://doi.org/10.1109/idaacs.2011.6072742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 6th IEEE International Conference on Intelligent Data Acquisition and Advanced Computing Systems","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1966078827","https://openalex.org/W1979364248","https://openalex.org/W1992092350","https://openalex.org/W2029667189","https://openalex.org/W2047799927","https://openalex.org/W2064714238","https://openalex.org/W2080700284","https://openalex.org/W2092939357","https://openalex.org/W2111676963","https://openalex.org/W2123182960","https://openalex.org/W2736581129","https://openalex.org/W6740994486"],"related_works":["https://openalex.org/W2356602486","https://openalex.org/W2351992668","https://openalex.org/W2324828474","https://openalex.org/W2374315191","https://openalex.org/W2391207559","https://openalex.org/W2384715785","https://openalex.org/W2349624418","https://openalex.org/W2064459023","https://openalex.org/W2384611437","https://openalex.org/W2907301531"],"abstract_inverted_index":{"Existing":[0],"molecular":[1,8,27,83],"modeling":[2,84],"software":[3,65],"and":[4,75],"different":[5],"techniques":[6,78],"of":[7,16,35,63,88,98],"dynamics":[9,28],"trajectories":[10],"analysis":[11,71],"were":[12,45,66,79],"evaluated":[13],"in":[14,43,93],"terms":[15],"subsequent":[17],"integration":[18],"into":[19],"the":[20,31,39],"MolDynGrid":[21,44,94],"virtual":[22],"laboratory":[23],"services.":[24],"GROMACS":[25],"4":[26],"package":[29],"contains":[30],"most":[32],"comprehensive":[33],"set":[34,97],"analytical":[36,41,89],"programs,":[37],"thus":[38],"standard":[40],"tools":[42],"based":[46],"on":[47],"this":[48],"software.":[49],"G_correlation":[50],"tool":[51],"was":[52,91],"ported":[53],"to":[54],"GPU":[55],"which":[56],"dramatically":[57],"increased":[58],"its":[59],"productivity.":[60],"Scripting":[61],"capabilities":[62],"VMD":[64],"used":[67],"for":[68],"certain":[69],"non-standard":[70],"techniques,":[72],"while":[73],"complex":[74],"computationally":[76],"intensive":[77],"implemented":[80,92],"using":[81],"Pteros":[82],"library.":[85],"Parallel":[86],"execution":[87],"programs":[90],"by":[95],"a":[96],"internally":[99],"developed":[100],"scripts.":[101]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
