{"id":"https://openalex.org/W2611907395","doi":"https://doi.org/10.1021/acs.jcim.6b00442","title":"HELM Software for Biopolymers","display_name":"HELM Software for Biopolymers","publication_year":2017,"publication_date":"2017-05-04","ids":{"openalex":"https://openalex.org/W2611907395","doi":"https://doi.org/10.1021/acs.jcim.6b00442","mag":"2611907395","pmid":"https://pubmed.ncbi.nlm.nih.gov/28471655"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00442","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00442","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5048499230","display_name":"Jeff Milton","orcid":"https://orcid.org/0000-0001-8160-1390"},"institutions":[{"id":"https://openalex.org/I2800035258","display_name":"Ionis Pharmaceuticals (United States)","ror":"https://ror.org/00t8bew53","country_code":"US","type":"company","lineage":["https://openalex.org/I2800035258"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeff Milton","raw_affiliation_strings":["Ionis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, California 92010, United States"],"affiliations":[{"raw_affiliation_string":"Ionis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, California 92010, United States","institution_ids":["https://openalex.org/I2800035258"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100624111","display_name":"Tianhong Zhang","orcid":"https://orcid.org/0000-0001-6599-8607"},"institutions":[{"id":"https://openalex.org/I180857899","display_name":"Pfizer (United States)","ror":"https://ror.org/01xdqrp08","country_code":"US","type":"company","lineage":["https://openalex.org/I180857899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianhong Zhang","raw_affiliation_strings":["Pfizer Inc., One Burtt Road, Andover, Massachusetts 01810, United States"],"affiliations":[{"raw_affiliation_string":"Pfizer Inc., One Burtt Road, Andover, Massachusetts 01810, United States","institution_ids":["https://openalex.org/I180857899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011756723","display_name":"Claire Bellamy","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Claire Bellamy","raw_affiliation_strings":["Pistoia Alliance, 401 Edgewater\rPlace, Wakefield, Massachusetts 01880-6201, United States"],"affiliations":[{"raw_affiliation_string":"Pistoia Alliance, 401 Edgewater\rPlace, Wakefield, Massachusetts 01880-6201, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009098620","display_name":"Eric E. Swayze","orcid":"https://orcid.org/0000-0001-6430-6576"},"institutions":[{"id":"https://openalex.org/I2800035258","display_name":"Ionis Pharmaceuticals (United States)","ror":"https://ror.org/00t8bew53","country_code":"US","type":"company","lineage":["https://openalex.org/I2800035258"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Swayze","raw_affiliation_strings":["Ionis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, California 92010, United States"],"affiliations":[{"raw_affiliation_string":"Ionis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, California 92010, United States","institution_ids":["https://openalex.org/I2800035258"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075216170","display_name":"Christopher E. Hart","orcid":"https://orcid.org/0000-0003-0726-5071"},"institutions":[{"id":"https://openalex.org/I2800035258","display_name":"Ionis Pharmaceuticals (United States)","ror":"https://ror.org/00t8bew53","country_code":"US","type":"company","lineage":["https://openalex.org/I2800035258"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Hart","raw_affiliation_strings":["Ionis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, California 92010, United States"],"affiliations":[{"raw_affiliation_string":"Ionis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, California 92010, United States","institution_ids":["https://openalex.org/I2800035258"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079451704","display_name":"Markus Weisser","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Markus Weisser","raw_affiliation_strings":["Quattro Research, Fraunhoferstra\u00dfe\r18a 82152 Planegg\u2212Martinsried, Germany"],"affiliations":[{"raw_affiliation_string":"Quattro Research, Fraunhoferstra\u00dfe\r18a 82152 Planegg\u2212Martinsried, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089258857","display_name":"Sabrina Hecht","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sabrina Hecht","raw_affiliation_strings":["Quattro Research, Fraunhoferstra\u00dfe\r18a 82152 Planegg\u2212Martinsried, Germany"],"affiliations":[{"raw_affiliation_string":"Quattro Research, Fraunhoferstra\u00dfe\r18a 82152 Planegg\u2212Martinsried, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063839992","display_name":"Sergio H. Rotstein","orcid":null},"institutions":[{"id":"https://openalex.org/I180857899","display_name":"Pfizer (United States)","ror":"https://ror.org/01xdqrp08","country_code":"US","type":"company","lineage":["https://openalex.org/I180857899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergio Rotstein","raw_affiliation_strings":["Pfizer Inc., One Burtt Road, Andover, Massachusetts 01810, United States"],"affiliations":[{"raw_affiliation_string":"Pfizer Inc., One Burtt Road, Andover, Massachusetts 01810, United States","institution_ids":["https://openalex.org/I180857899"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5048499230"],"corresponding_institution_ids":["https://openalex.org/I2800035258"],"apc_list":null,"apc_paid":null,"fwci":0.7232,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.65395999,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"57","issue":"6","first_page":"1233","last_page":"1239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T11162","display_name":"Enzyme Structure and Function","score":0.9861999750137329,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9804999828338623,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6397459506988525},{"id":"https://openalex.org/keywords/notation","display_name":"Notation","score":0.6375133395195007},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5635064840316772},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.46128931641578674},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3844999372959137},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.251573383808136},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.08854520320892334},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.06807354092597961}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6397459506988525},{"id":"https://openalex.org/C45357846","wikidata":"https://www.wikidata.org/wiki/Q2001982","display_name":"Notation","level":2,"score":0.6375133395195007},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5635064840316772},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.46128931641578674},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3844999372959137},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.251573383808136},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.08854520320892334},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.06807354092597961}],"mesh":[{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00442","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00442","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:28471655","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28471655","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W186225224","https://openalex.org/W1495543934","https://openalex.org/W1508604947","https://openalex.org/W1919927381","https://openalex.org/W1989294176","https://openalex.org/W1998612140","https://openalex.org/W2026677671","https://openalex.org/W2083224653","https://openalex.org/W2090401806","https://openalex.org/W2110455859","https://openalex.org/W2121137483","https://openalex.org/W2128557878","https://openalex.org/W2137906189","https://openalex.org/W2330089088","https://openalex.org/W2382347082"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2504004674","https://openalex.org/W2963177394","https://openalex.org/W2498744856","https://openalex.org/W4390482104","https://openalex.org/W322408318","https://openalex.org/W149041114","https://openalex.org/W2390279801","https://openalex.org/W1965815883"],"abstract_inverted_index":{"Hierarchical":[0],"Editing":[1],"Language":[2],"for":[3,18,87],"Macromolecules":[4],"(HELM":[5],"version":[6,50],"2.0)":[7],"is":[8],"a":[9,43,81,91,97],"molecular":[10,100],"line":[11],"notation":[12,65],"similar":[13],"to":[14,37,73,95],"SMILEs":[15],"but":[16],"specifically":[17],"communicating":[19],"and":[20,39,47,85,90],"managing":[21],"biopolymer":[22],"structures.":[23],"The":[24],"HELM":[25,41,63,88],"project,":[26],"part":[27],"of":[28,52,61,71],"the":[29,53,59,62,68],"Pistoia":[30],"Alliance":[31],"nonprofit":[32],"organization,":[33],"has":[34],"been":[35],"tasked":[36],"develop":[38],"promote":[40],"as":[42],"global":[44],"exchange":[45],"format":[46],"recently":[48],"released":[49],"2.0":[51],"specification.":[54],"Here":[55],"we":[56],"will":[57,79],"describe":[58],"specifics":[60],"v2.0":[64],"along":[66],"with":[67],"large":[69,98],"ecosystem":[70],"software":[72,84],"support":[74],"HELM-based":[75],"structure":[76],"management.":[77],"We":[78],"highlight":[80],"recent":[82],"open-source":[83],"database":[86],"monomers":[89],"new,":[92],"simpler":[93],"approach":[94],"deploying":[96],"complicated":[99],"management":[101],"system.":[102]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
