{"id":"https://openalex.org/W2081575273","doi":"https://doi.org/10.1021/ci200141j","title":"Molecular Dynamics Simulation and Binding Energy Calculation for Estimation of Oligonucleotide Duplex Thermostability in RNA-Based Therapeutics","display_name":"Molecular Dynamics Simulation and Binding Energy Calculation for Estimation of Oligonucleotide Duplex Thermostability in RNA-Based Therapeutics","publication_year":2011,"publication_date":"2011-06-25","ids":{"openalex":"https://openalex.org/W2081575273","doi":"https://doi.org/10.1021/ci200141j","mag":"2081575273","pmid":"https://pubmed.ncbi.nlm.nih.gov/21702481"},"language":"en","primary_location":{"id":"doi:10.1021/ci200141j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200141j","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/A5082001475","display_name":"Lingling Shen","orcid":"https://orcid.org/0000-0003-1246-1413"},"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":true,"raw_author_name":"Lingling Shen","raw_affiliation_strings":["Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States"],"affiliations":[{"raw_affiliation_string":"Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States","institution_ids":["https://openalex.org/I180857899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035249855","display_name":"Theresa Johnson","orcid":"https://orcid.org/0000-0002-7406-4168"},"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":"Theresa L. Johnson","raw_affiliation_strings":["Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States"],"affiliations":[{"raw_affiliation_string":"Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States","institution_ids":["https://openalex.org/I180857899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043678705","display_name":"Susan L. Clugston","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":"Susan Clugston","raw_affiliation_strings":["Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States"],"affiliations":[{"raw_affiliation_string":"Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States","institution_ids":["https://openalex.org/I180857899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103169536","display_name":"Hongwei Huang","orcid":"https://orcid.org/0000-0001-8269-4461"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hongwei Huang","raw_affiliation_strings":["Accelrys, 200 Wheeler Road, South Tower, Second Floor, Burlington, Massachusetts 01803, United States"],"affiliations":[{"raw_affiliation_string":"Accelrys, 200 Wheeler Road, South Tower, Second Floor, Burlington, Massachusetts 01803, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021929633","display_name":"Kenneth J. Butenhof","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kenneth J. Butenhof","raw_affiliation_strings":["Accelrys, 200 Wheeler Road, South Tower, Second Floor, Burlington, Massachusetts 01803, United States"],"affiliations":[{"raw_affiliation_string":"Accelrys, 200 Wheeler Road, South Tower, Second Floor, Burlington, Massachusetts 01803, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047169849","display_name":"Robert V. Stanton","orcid":"https://orcid.org/0000-0002-4989-6958"},"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":"Robert V. Stanton","raw_affiliation_strings":["Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States"],"affiliations":[{"raw_affiliation_string":"Pfizer, 620 Memorial Drive, Cambridge, Massachusetts 02139, United States","institution_ids":["https://openalex.org/I180857899"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5082001475"],"corresponding_institution_ids":["https://openalex.org/I180857899"],"apc_list":null,"apc_paid":null,"fwci":0.5211,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.65369979,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"51","issue":"8","first_page":"1957","last_page":"1965"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9998000264167786,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9998000264167786,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9986000061035156,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9966999888420105,"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/oligonucleotide","display_name":"Oligonucleotide","score":0.8849146366119385},{"id":"https://openalex.org/keywords/thermostability","display_name":"Thermostability","score":0.7507154941558838},{"id":"https://openalex.org/keywords/duplex","display_name":"Duplex (building)","score":0.7322144508361816},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6037800908088684},{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.5787897706031799},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5482561588287354},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4830487370491028},{"id":"https://openalex.org/keywords/locked-nucleic-acid","display_name":"Locked nucleic acid","score":0.4808509945869446},{"id":"https://openalex.org/keywords/small-interfering-rna","display_name":"Small interfering RNA","score":0.46440720558166504},{"id":"https://openalex.org/keywords/melting-temperature","display_name":"Melting temperature","score":0.4326780438423157},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43064606189727783},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3555797338485718},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3488442003726959},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2652791142463684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24800947308540344},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1932404339313507},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16135111451148987},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1573907732963562}],"concepts":[{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.8849146366119385},{"id":"https://openalex.org/C2781216036","wikidata":"https://www.wikidata.org/wiki/Q902494","display_name":"Thermostability","level":3,"score":0.7507154941558838},{"id":"https://openalex.org/C99611785","wikidata":"https://www.wikidata.org/wiki/Q6453233","display_name":"Duplex (building)","level":3,"score":0.7322144508361816},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6037800908088684},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.5787897706031799},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5482561588287354},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4830487370491028},{"id":"https://openalex.org/C14363569","wikidata":"https://www.wikidata.org/wiki/Q418639","display_name":"Locked nucleic acid","level":4,"score":0.4808509945869446},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.46440720558166504},{"id":"https://openalex.org/C2985276288","wikidata":"https://www.wikidata.org/wiki/Q16873139","display_name":"Melting temperature","level":2,"score":0.4326780438423157},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43064606189727783},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3555797338485718},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3488442003726959},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2652791142463684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24800947308540344},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1932404339313507},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16135111451148987},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1573907732963562},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D002626","descriptor_name":"Chemistry, Pharmaceutical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002626","descriptor_name":"Chemistry, Pharmaceutical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002626","descriptor_name":"Chemistry, Pharmaceutical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004355","descriptor_name":"Drug Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004355","descriptor_name":"Drug Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004355","descriptor_name":"Drug Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009692","descriptor_name":"Nucleic Acid Heteroduplexes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009692","descriptor_name":"Nucleic Acid Heteroduplexes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009692","descriptor_name":"Nucleic Acid Heteroduplexes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009692","descriptor_name":"Nucleic Acid Heteroduplexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009692","descriptor_name":"Nucleic Acid Heteroduplexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009692","descriptor_name":"Nucleic Acid Heteroduplexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013053","descriptor_name":"Spectrophotometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013053","descriptor_name":"Spectrophotometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013053","descriptor_name":"Spectrophotometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015316","descriptor_name":"Genetic Therapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015316","descriptor_name":"Genetic Therapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015316","descriptor_name":"Genetic Therapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016376","descriptor_name":"Oligonucleotides, Antisense","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D044366","descriptor_name":"Transition Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044366","descriptor_name":"Transition Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044366","descriptor_name":"Transition Temperature","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057205","descriptor_name":"Automation, Laboratory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057205","descriptor_name":"Automation, Laboratory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057205","descriptor_name":"Automation, Laboratory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058990","descriptor_name":"Molecular Targeted Therapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058990","descriptor_name":"Molecular Targeted Therapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058990","descriptor_name":"Molecular Targeted Therapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200141j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200141j","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:21702481","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21702481","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":[{"display_name":"Affordable and clean energy","score":0.8600000143051147,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1489972628","https://openalex.org/W1647075334","https://openalex.org/W1959245158","https://openalex.org/W1961408670","https://openalex.org/W1967737979","https://openalex.org/W1976266243","https://openalex.org/W1976499671","https://openalex.org/W1981430299","https://openalex.org/W2009215649","https://openalex.org/W2010759469","https://openalex.org/W2016531498","https://openalex.org/W2017829285","https://openalex.org/W2032852295","https://openalex.org/W2051713039","https://openalex.org/W2055827668","https://openalex.org/W2070171578","https://openalex.org/W2081407973","https://openalex.org/W2095145098","https://openalex.org/W2106140689","https://openalex.org/W2110811598","https://openalex.org/W2112829828","https://openalex.org/W2113368761","https://openalex.org/W2116282666","https://openalex.org/W2117620409","https://openalex.org/W2121133384","https://openalex.org/W2122885496","https://openalex.org/W2129055358","https://openalex.org/W2132262459","https://openalex.org/W2133620923","https://openalex.org/W2135995702","https://openalex.org/W2138825634","https://openalex.org/W2139273728","https://openalex.org/W2141525074","https://openalex.org/W2145269229","https://openalex.org/W2162166182","https://openalex.org/W2163987996","https://openalex.org/W2164497648","https://openalex.org/W2169256371","https://openalex.org/W4232855656"],"related_works":["https://openalex.org/W2017658021","https://openalex.org/W2100333422","https://openalex.org/W2118381199","https://openalex.org/W1985072032","https://openalex.org/W1990497029","https://openalex.org/W4243220568","https://openalex.org/W2009215649","https://openalex.org/W3024785073","https://openalex.org/W2054642120","https://openalex.org/W1988423615"],"abstract_inverted_index":{"For":[0,21],"oligonucleotide-based":[1],"therapeutics,":[2],"a":[3,103,112],"thorough":[4],"understanding":[5],"of":[6,10,77,89,102,137],"the":[7,75,87,90,94,123,135,138],"thermodynamic":[8,53],"properties":[9,54],"duplex":[11,52,96],"formation":[12],"is":[13],"critical":[14],"to":[15,47],"developing":[16],"stable":[17],"and":[18,31,49,146,150],"potent":[19],"drugs.":[20],"unmodified":[22],"small":[23],"interfering":[24],"RNA":[25],"(siRNA),":[26],"DNA":[27],"antisense":[28],"oligonucleotide":[29],"(AON)":[30],"locked":[32],"nucleic":[33],"acid":[34],"(LNA),":[35],"DNA/LNA":[36],"modified":[37,62,148],"oligonucleotides,":[38],"nearest":[39],"neighbor":[40],"(NN)":[41],"methods":[42],"can":[43],"be":[44,132],"effectively":[45],"used":[46],"quickly":[48],"accurately":[50],"predict":[51],"such":[55],"as":[56],"melting":[57,79],"point.":[58],"Unfortunately,":[59],"for":[60,82,100,143],"chemically":[61,147],"olignonucleotides,":[63],"there":[64],"has":[65,108],"been":[66,109],"no":[67],"accurate":[68],"prediction":[69],"method":[70,107],"available.":[71],"Here":[72],"we":[73],"describe":[74],"potential":[76],"estimating":[78],"temperature":[80],"(T(m))":[81],"nonstandard":[83],"oligonucleotides":[84,101],"by":[85],"using":[86,122],"correlation":[88,136],"experimental":[91],"T(m)":[92],"with":[93,141],"calculated":[95],"binding":[97],"energy":[98],"(BE)":[99],"given":[104],"length.":[105],"This":[106],"automated":[110],"into":[111],"standardized":[113],"molecular":[114],"dynamics":[115],"(MD)":[116],"protocol":[117],"through":[118],"Pipeline":[119],"Pilot":[120],"(PP)":[121],"CHARMm":[124],"component":[125],"in":[126],"Discovery":[127],"Studio":[128],"(DS).":[129],"Results":[130],"will":[131],"presented":[133],"showing":[134],"predicted":[139],"data":[140],"experiment":[142],"both":[144],"standard":[145],"siRNA":[149],"AON.":[151]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}