{"id":"https://openalex.org/W2970916026","doi":"https://doi.org/10.1145/3352700.3352701","title":"A Protein Structure Prediction Program Architecture Based on a Software Transactional Memory","display_name":"A Protein Structure Prediction Program Architecture Based on a Software Transactional Memory","publication_year":2019,"publication_date":"2019-08-28","ids":{"openalex":"https://openalex.org/W2970916026","doi":"https://doi.org/10.1145/3352700.3352701","mag":"2970916026"},"language":"en","primary_location":{"id":"doi:10.1145/3352700.3352701","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3352700.3352701","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 Conference on the Engineering of Computer Based 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/A5069129540","display_name":"Branislav Kordic","orcid":null},"institutions":[{"id":"https://openalex.org/I170726198","display_name":"University of Novi Sad","ror":"https://ror.org/00xa57a59","country_code":"RS","type":"education","lineage":["https://openalex.org/I170726198"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Branislav Kordic","raw_affiliation_strings":["University of Novi Sad, Novi Sad, Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Novi Sad, Novi Sad, Serbia","institution_ids":["https://openalex.org/I170726198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102991154","display_name":"Marko Popovi\u0107","orcid":"https://orcid.org/0000-0002-1957-0092"},"institutions":[{"id":"https://openalex.org/I170726198","display_name":"University of Novi Sad","ror":"https://ror.org/00xa57a59","country_code":"RS","type":"education","lineage":["https://openalex.org/I170726198"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Marko Popovic","raw_affiliation_strings":["University of Novi Sad, Novi Sad, Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Novi Sad, Novi Sad, Serbia","institution_ids":["https://openalex.org/I170726198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074956004","display_name":"Miroslav Popovi\u0107","orcid":"https://orcid.org/0000-0001-8385-149X"},"institutions":[{"id":"https://openalex.org/I170726198","display_name":"University of Novi Sad","ror":"https://ror.org/00xa57a59","country_code":"RS","type":"education","lineage":["https://openalex.org/I170726198"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Miroslav Popovic","raw_affiliation_strings":["University of Novi Sad, Novi Sad, Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Novi Sad, Novi Sad, Serbia","institution_ids":["https://openalex.org/I170726198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059097596","display_name":"Moshe Goldstein","orcid":"https://orcid.org/0000-0002-0429-4873"},"institutions":[{"id":"https://openalex.org/I192238737","display_name":"Jerusalem College of Technology","ror":"https://ror.org/002kenh51","country_code":"IL","type":"education","lineage":["https://openalex.org/I192238737"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Moshe Goldstein","raw_affiliation_strings":["Department of Computer Science, Jerusalem College of Technology, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Jerusalem College of Technology, Jerusalem, Israel","institution_ids":["https://openalex.org/I192238737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068827723","display_name":"Moshe Amitay","orcid":"https://orcid.org/0000-0002-6897-9580"},"institutions":[{"id":"https://openalex.org/I192238737","display_name":"Jerusalem College of Technology","ror":"https://ror.org/002kenh51","country_code":"IL","type":"education","lineage":["https://openalex.org/I192238737"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Moshe Amitay","raw_affiliation_strings":["Department of Bioinformatics, Jerusalem College of Technology, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Jerusalem College of Technology, Jerusalem, Israel","institution_ids":["https://openalex.org/I192238737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014318124","display_name":"David Dayan","orcid":null},"institutions":[{"id":"https://openalex.org/I192238737","display_name":"Jerusalem College of Technology","ror":"https://ror.org/002kenh51","country_code":"IL","type":"education","lineage":["https://openalex.org/I192238737"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"David Dayan","raw_affiliation_strings":["Department of Computer Science, Jerusalem College of Technology, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Jerusalem College of Technology, Jerusalem, Israel","institution_ids":["https://openalex.org/I192238737"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.186,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.55882916,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10772","display_name":"Distributed systems and fault tolerance","score":0.9940000176429749,"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/T10772","display_name":"Distributed systems and fault tolerance","score":0.9940000176429749,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9886000156402588,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T10829","display_name":"Interconnection Networks and Systems","score":0.98580002784729,"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":0.8657345771789551},{"id":"https://openalex.org/keywords/software-transactional-memory","display_name":"Software transactional memory","score":0.8586373329162598},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7327026128768921},{"id":"https://openalex.org/keywords/transactional-memory","display_name":"Transactional memory","score":0.5949149131774902},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5758184194564819},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.49229443073272705},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.45809584856033325},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4391992688179016},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.42831629514694214},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41013091802597046},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3885756731033325},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3424440026283264},{"id":"https://openalex.org/keywords/database-transaction","display_name":"Database transaction","score":0.17521202564239502}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8657345771789551},{"id":"https://openalex.org/C167149655","wikidata":"https://www.wikidata.org/wiki/Q1189004","display_name":"Software transactional memory","level":4,"score":0.8586373329162598},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7327026128768921},{"id":"https://openalex.org/C134277064","wikidata":"https://www.wikidata.org/wiki/Q878206","display_name":"Transactional memory","level":3,"score":0.5949149131774902},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5758184194564819},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.49229443073272705},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.45809584856033325},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4391992688179016},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.42831629514694214},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41013091802597046},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3885756731033325},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3424440026283264},{"id":"https://openalex.org/C75949130","wikidata":"https://www.wikidata.org/wiki/Q848010","display_name":"Database transaction","level":2,"score":0.17521202564239502},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3352700.3352701","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3352700.3352701","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 Conference on the Engineering of Computer Based Systems","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W59694360","https://openalex.org/W98056105","https://openalex.org/W1496687288","https://openalex.org/W1515765480","https://openalex.org/W1967925841","https://openalex.org/W2024060531","https://openalex.org/W2051434435","https://openalex.org/W2062796765","https://openalex.org/W2080675607","https://openalex.org/W2089591371","https://openalex.org/W2091914261","https://openalex.org/W2092911542","https://openalex.org/W2094222793","https://openalex.org/W2103933790","https://openalex.org/W2113751407","https://openalex.org/W2150732552","https://openalex.org/W2154468535","https://openalex.org/W2163654949","https://openalex.org/W2477724447","https://openalex.org/W2580666741","https://openalex.org/W2748582957","https://openalex.org/W2785694006","https://openalex.org/W2789441477","https://openalex.org/W2802710827","https://openalex.org/W3005522790","https://openalex.org/W3028664549","https://openalex.org/W3149025087","https://openalex.org/W6673307265","https://openalex.org/W6749223495","https://openalex.org/W6751040124"],"related_works":["https://openalex.org/W2088444093","https://openalex.org/W133473147","https://openalex.org/W4252722439","https://openalex.org/W924353067","https://openalex.org/W2152491655","https://openalex.org/W2992926879","https://openalex.org/W1144911151","https://openalex.org/W2076409732","https://openalex.org/W120707803","https://openalex.org/W2104221844"],"abstract_inverted_index":{"As":[0],"an":[1,44],"alternative":[2],"for":[3,33,54,87],"traditional":[4],"lock-based":[5],"synchronization":[6,71],"mechanisms":[7],"Software":[8,145],"Transactional":[9,146],"Memories":[10],"(STMs)":[11],"are":[12,153],"dominantly":[13],"evaluated":[14,154],"on":[15,23,228,242],"synthetic":[16],"benchmarks":[17],"and":[18,35,81,103,130,160,182],"simplified":[19],"applications":[20],"rather":[21],"than":[22],"real-world":[24],"applications.":[25],"So":[26],"far,":[27],"only":[28],"a":[29,48,229,243],"few":[30],"notable":[31],"examples":[32],"C++":[34],"JAVA":[36],"languages":[37],"have":[38],"been":[39],"published.":[40],"In":[41,222],"this":[42,193],"paper,":[43],"STM-based":[45,61],"architecture":[46,62,185],"of":[47,77,93,171,192,206,247],"Protein":[49],"Structure":[50],"Prediction":[51],"(PSP)":[52],"program":[53,112],"the":[55,67,74,84,94,99,104,128,167,179,190,203],"Python":[56,129,148],"language":[57],"is":[58,107,115,125,141],"presented.":[59],"This":[60],"aims":[63],"both,":[64],"to":[65,82,178,224],"enhance":[66],"existing":[68],"barrier-based":[69],"process":[70],"implemented":[72,126],"in":[73,127,211,251],"original":[75,180,204],"version":[76,170,205],"that":[78,166,183,202],"PSP":[79,111],"program,":[80],"provide":[83],"transactional-memory-based":[85],"means":[86],"its":[88,184],"future":[89],"upgrade.":[90],"The":[91,110,134,150,162],"analysis":[92],"performance":[95],"metrics,":[96],"such":[97,232],"as":[98,233],"system":[100,105],"execution":[101,140,175,217,236],"time":[102,176],"scalability,":[106],"given":[108],"too.":[109],"used":[113],"here":[114],"DEEPSAM":[116,172,207],"(Diffusion":[117],"Equation":[118],"Evolutionary":[119],"Programming":[120],"Simulated":[121],"Annealing":[122],"Method)":[123],"which":[124,137],"Fortran":[131],"programing":[132],"languages.":[133],"key":[135],"component":[136],"supports":[138],"transactional":[139],"our":[142],"PSTM":[143],"(Python":[144],"Memory)":[147],"framework.":[149],"experimental":[151],"results":[152,164,191],"against":[155],"two":[156],"peptides,":[157],"namely":[158],"enkephalin":[159],"2mq5.":[161],"preliminary":[163],"show":[165],"new":[168],"PSTM-based":[169],"has":[173],"comparable":[174],"relative":[177],"version,":[181],"scales":[186],"very":[187],"well.":[188],"Also,":[189],"study":[194],"did":[195],"not":[196,220],"reveal":[197],"any":[198],"architectural":[199],"bottleneck.":[200],"Considering":[201],"already":[208],"execute":[209],"computation":[210],"parallel,":[212],"gaining":[213],"significant":[214],"improvements":[215],"regarding":[216,235],"times":[218],"was":[219],"expected.":[221],"order":[223],"comprehend":[225],"PSTM's":[226],"impact":[227],"complex":[230],"package":[231],"DEEPSAM,":[234],"times,":[237],"it":[238],"must":[239],"be":[240],"run":[241],"many-core":[244],"processor":[245],"capable":[246],"running":[248],"dozens":[249],"processes":[250],"parallel.":[252]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}