{"id":"https://openalex.org/W4399283745","doi":"https://doi.org/10.1021/acs.jcim.4c00077","title":"Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities","display_name":"Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities","publication_year":2024,"publication_date":"2024-06-03","ids":{"openalex":"https://openalex.org/W4399283745","doi":"https://doi.org/10.1021/acs.jcim.4c00077","pmid":"https://pubmed.ncbi.nlm.nih.gov/38829726"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00077","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00077","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/A5040480267","display_name":"Ethan Berger","orcid":"https://orcid.org/0000-0001-9143-4493"},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ethan Berger","raw_affiliation_strings":["Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland"],"raw_orcid":"https://orcid.org/0000-0001-9143-4493","affiliations":[{"raw_affiliation_string":"Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113107520","display_name":"Juha Niemel\u00e4","orcid":null},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Juha Niemel\u00e4","raw_affiliation_strings":["Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033941308","display_name":"Outi Lampela","orcid":null},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Outi Lampela","raw_affiliation_strings":["Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014,  Finland","Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014,  Finland","institution_ids":["https://openalex.org/I98381234"]},{"raw_affiliation_string":"Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035246521","display_name":"Andr\u00e9 H. Juffer","orcid":"https://orcid.org/0000-0003-3533-0520"},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 H. Juffer","raw_affiliation_strings":["Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014,  Finland","Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014,  Finland","institution_ids":["https://openalex.org/I98381234"]},{"raw_affiliation_string":"Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013900222","display_name":"Hannu\u2010Pekka Komsa","orcid":"https://orcid.org/0000-0002-0970-0957"},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Hannu-Pekka Komsa","raw_affiliation_strings":["Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland"],"raw_orcid":"https://orcid.org/0000-0002-0970-0957","affiliations":[{"raw_affiliation_string":"Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland","institution_ids":["https://openalex.org/I98381234"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5013900222"],"corresponding_institution_ids":["https://openalex.org/I98381234"],"apc_list":null,"apc_paid":null,"fwci":7.5793,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.96863488,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"64","issue":"12","first_page":"4601","last_page":"4612"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11324","display_name":"Spectroscopy Techniques in Biomedical and Chemical Research","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11324","display_name":"Spectroscopy Techniques in Biomedical and Chemical Research","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9962999820709229,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/raman-spectroscopy","display_name":"Raman spectroscopy","score":0.667447030544281},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5784586668014526},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.44667619466781616},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3692626655101776},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3359188437461853},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2797781527042389},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23083525896072388},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22458350658416748},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2105257511138916},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.12243801355361938}],"concepts":[{"id":"https://openalex.org/C40003534","wikidata":"https://www.wikidata.org/wiki/Q862228","display_name":"Raman spectroscopy","level":2,"score":0.667447030544281},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5784586668014526},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.44667619466781616},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3692626655101776},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3359188437461853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2797781527042389},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23083525896072388},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22458350658416748},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2105257511138916},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.12243801355361938}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077318","descriptor_name":"Density Functional Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077318","descriptor_name":"Density Functional Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077318","descriptor_name":"Density Functional Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013059","descriptor_name":"Spectrum Analysis, Raman","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013059","descriptor_name":"Spectrum Analysis, Raman","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013059","descriptor_name":"Spectrum Analysis, Raman","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c00077","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00077","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:38829726","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38829726","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":"Quality Education","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2450994528","display_name":null,"funder_award_id":"357483","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7695122763","display_name":"Machine-learned polarizability for Raman spectra of complex materials","funder_award_id":"357483","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":104,"referenced_works":["https://openalex.org/W1518071694","https://openalex.org/W1963638325","https://openalex.org/W1972135189","https://openalex.org/W1976499671","https://openalex.org/W1977584896","https://openalex.org/W1978498560","https://openalex.org/W1982952953","https://openalex.org/W1989060947","https://openalex.org/W1995147105","https://openalex.org/W1996384061","https://openalex.org/W1999225355","https://openalex.org/W2000621548","https://openalex.org/W2000770615","https://openalex.org/W2003423687","https://openalex.org/W2010051841","https://openalex.org/W2014166972","https://openalex.org/W2019916133","https://openalex.org/W2025444507","https://openalex.org/W2025833310","https://openalex.org/W2027038798","https://openalex.org/W2029413789","https://openalex.org/W2034786972","https://openalex.org/W2051287579","https://openalex.org/W2052038479","https://openalex.org/W2054765464","https://openalex.org/W2054767491","https://openalex.org/W2057477511","https://openalex.org/W2057554431","https://openalex.org/W2062156487","https://openalex.org/W2062785845","https://openalex.org/W2064685925","https://openalex.org/W2067174909","https://openalex.org/W2075122788","https://openalex.org/W2078118504","https://openalex.org/W2081254445","https://openalex.org/W2081693079","https://openalex.org/W2083415705","https://openalex.org/W2089888531","https://openalex.org/W2106025186","https://openalex.org/W2110300847","https://openalex.org/W2128298256","https://openalex.org/W2137875704","https://openalex.org/W2148284063","https://openalex.org/W2156186217","https://openalex.org/W2167132383","https://openalex.org/W2171268876","https://openalex.org/W2312422579","https://openalex.org/W2335130470","https://openalex.org/W2337496963","https://openalex.org/W2566642125","https://openalex.org/W2736127891","https://openalex.org/W2757878424","https://openalex.org/W2771560613","https://openalex.org/W2773437515","https://openalex.org/W2884914945","https://openalex.org/W2891523768","https://openalex.org/W2922733622","https://openalex.org/W2943626891","https://openalex.org/W2953168127","https://openalex.org/W2972006524","https://openalex.org/W2992288658","https://openalex.org/W3013594480","https://openalex.org/W3013697879","https://openalex.org/W3014525631","https://openalex.org/W3015915882","https://openalex.org/W3022120464","https://openalex.org/W3027308092","https://openalex.org/W3033994814","https://openalex.org/W3081527099","https://openalex.org/W3084211373","https://openalex.org/W3095157427","https://openalex.org/W3100839762","https://openalex.org/W3101744365","https://openalex.org/W3102389151","https://openalex.org/W3102870719","https://openalex.org/W3134779976","https://openalex.org/W3141927472","https://openalex.org/W3153640338","https://openalex.org/W3161387365","https://openalex.org/W3185465747","https://openalex.org/W3189164715","https://openalex.org/W3199616379","https://openalex.org/W3199681061","https://openalex.org/W3200818036","https://openalex.org/W3201839586","https://openalex.org/W3207040922","https://openalex.org/W4210943698","https://openalex.org/W4211237647","https://openalex.org/W4214705575","https://openalex.org/W4252104217","https://openalex.org/W4281385937","https://openalex.org/W4286588524","https://openalex.org/W4290805632","https://openalex.org/W4310570877","https://openalex.org/W4316038721","https://openalex.org/W4317938386","https://openalex.org/W4319459731","https://openalex.org/W4319597895","https://openalex.org/W4362522009","https://openalex.org/W4377221266","https://openalex.org/W4383187091","https://openalex.org/W4393869900","https://openalex.org/W4393935317","https://openalex.org/W4394767253"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"Raman":[0,20,128],"spectroscopy":[1],"is":[2,62,70],"an":[3],"important":[4],"tool":[5],"in":[6,172],"the":[7,27,30,50,53,85,106,161],"study":[8],"of":[9,14,29,52,87,118,130],"vibrational":[10],"properties":[11],"and":[12,17,64,97,137],"composition":[13],"molecules,":[15],"peptides,":[16],"even":[18,167],"proteins.":[19],"spectra":[21,129],"can":[22,36],"be":[23,38],"simulated":[24],"based":[25],"on":[26,46,56,67],"change":[28],"electronic":[31],"polarizability":[32],"with":[33,105,122,142],"vibrations,":[34],"which":[35],"nowadays":[37],"efficiently":[39],"obtained":[40,136],"via":[41],"machine":[42,80,119],"learning":[43,81,120],"models":[44,54,82,93,121,145],"trained":[45,55],"first-principles":[47],"data.":[48],"However,":[49],"transferability":[51],"small":[57,150],"molecules":[58],"to":[59,83,99,112,149,160],"larger":[60],"structures":[61,69,156],"unclear,":[63],"direct":[65],"training":[66,162,173],"large":[68],"prohibitively":[71],"expensive.":[72],"In":[73],"this":[74],"work,":[75],"we":[76],"first":[77],"train":[78],"two":[79],"predict":[84],"polarizabilities":[86],"all":[88,131],"20":[89],"amino":[90,132],"acids.":[91],"Both":[92],"are":[94,134,146],"carefully":[95],"benchmarked":[96],"compared":[98],"density":[100],"functional":[101],"theory":[102],"(DFT)":[103],"calculations,":[104],"neural":[107],"network":[108],"method":[109],"being":[110],"found":[111],"offer":[113],"better":[114],"transferability.":[115],"By":[116],"combination":[117],"classical":[123],"force":[124],"field":[125],"molecular":[126],"dynamics,":[127],"acids":[133],"also":[135],"investigated,":[138],"showing":[139],"good":[140],"agreement":[141],"experiments.":[143],"The":[144],"further":[147],"extended":[148],"peptides.":[151],"We":[152],"find":[153],"that":[154],"adding":[155],"containing":[157],"peptide":[158],"bonds":[159],"set":[163],"greatly":[164],"improves":[165],"predictions,":[166],"for":[168],"peptides":[169],"not":[170],"included":[171],"sets.":[174]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-10T14:10:52.464848","created_date":"2025-10-10T00:00:00"}
