{"id":"https://openalex.org/W2010830730","doi":"https://doi.org/10.1073/pnas.0510420103","title":"Intrinsic backbone preferences are fully present in blocked amino acids","display_name":"Intrinsic backbone preferences are fully present in blocked amino acids","publication_year":2006,"publication_date":"2006-01-19","ids":{"openalex":"https://openalex.org/W2010830730","doi":"https://doi.org/10.1073/pnas.0510420103","mag":"2010830730","pmid":"https://pubmed.ncbi.nlm.nih.gov/16423894","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/1360578"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.0510420103","doi":"https://doi.org/10.1073/pnas.0510420103","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.0510420103","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://europepmc.org/pmc/articles/PMC1360578","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000743525","display_name":"Franc Avbelj","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI","US"],"is_corresponding":false,"raw_author_name":"Franc Avbelj","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050749209","display_name":"Simona Goli\u010d Grdadolnik","orcid":"https://orcid.org/0000-0002-0873-9593","observed_orcids":["https://orcid.org/0000-0002-0873-9593"]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI","US"],"is_corresponding":false,"raw_author_name":"Simona Golic Grdadolnik","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027480921","display_name":"Jo\u017ee Grdadolnik","orcid":"https://orcid.org/0000-0002-0312-168X","observed_orcids":["https://orcid.org/0000-0002-0312-168X"]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI","US"],"is_corresponding":false,"raw_author_name":"Joze Grdadolnik","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I4210152560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109528346","display_name":"Robert L. Baldwin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI","US"],"is_corresponding":false,"raw_author_name":"Robert L. Baldwin","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI 1001 Ljubljana, Slovenia; and Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305-5307","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I4210152560"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.3579,"has_fulltext":false,"cited_by_count":122,"citation_normalized_percentile":{"value":0.88056702,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"103","issue":"5","first_page":"1272","last_page":"1277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9678000211715698,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9678000211715698,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.016100000590085983,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"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/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.007899999618530273,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dipeptides","display_name":"dipeptides","score":0.9330000281333923},{"id":"https://openalex.org/keywords/alanine-dipeptide","display_name":"alanine dipeptide","score":0.8840000033378601},{"id":"https://openalex.org/keywords/peptide-conformation","display_name":"peptide conformation","score":0.5839999914169312}],"concepts":[{"id":"https://openalex.org/C2779138802","wikidata":"https://www.wikidata.org/wiki/Q418602","display_name":"Dipeptide","level":3,"score":0.9222815632820129},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7674270868301392},{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.6491634249687195},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.6357371807098389},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5817340612411499},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5634424686431885},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.5286736488342285},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.4692758619785309},{"id":"https://openalex.org/C2779856020","wikidata":"https://www.wikidata.org/wiki/Q218642","display_name":"Alanine","level":3,"score":0.4263223111629486},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.408651202917099},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.20756447315216064},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.13532140851020813},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000409","descriptor_name":"Alanine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011489","descriptor_name":"Protein Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1073/pnas.0510420103","doi":"https://doi.org/10.1073/pnas.0510420103","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.0510420103","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:295192","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1360578","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1360578","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1360578","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"Proc Natl Acad Sci U S A","raw_type":"Text"},{"id":"pmid:16423894","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16423894","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,"listed_in":[],"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":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:295192","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1360578","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W27727037","https://openalex.org/W232800751","https://openalex.org/W252174905","https://openalex.org/W1498352465","https://openalex.org/W1510998615","https://openalex.org/W1536836616","https://openalex.org/W1963667773","https://openalex.org/W1968712781","https://openalex.org/W1977251828","https://openalex.org/W1981134448","https://openalex.org/W1984297493","https://openalex.org/W1990719397","https://openalex.org/W1999479012","https://openalex.org/W2002045092","https://openalex.org/W2010359485","https://openalex.org/W2011378420","https://openalex.org/W2025097726","https://openalex.org/W2025805963","https://openalex.org/W2026729332","https://openalex.org/W2026946969","https://openalex.org/W2028006120","https://openalex.org/W2029325972","https://openalex.org/W2035022967","https://openalex.org/W2050333027","https://openalex.org/W2050724948","https://openalex.org/W2057456885","https://openalex.org/W2058454436","https://openalex.org/W2060387789","https://openalex.org/W2060700734","https://openalex.org/W2064018465","https://openalex.org/W2068994001","https://openalex.org/W2075369230","https://openalex.org/W2080796053","https://openalex.org/W2083232514","https://openalex.org/W2106881092","https://openalex.org/W2113270377","https://openalex.org/W2123743163","https://openalex.org/W2129071110","https://openalex.org/W2139156723","https://openalex.org/W2151252209","https://openalex.org/W2152120207","https://openalex.org/W2154338322","https://openalex.org/W2160050027","https://openalex.org/W2161763549","https://openalex.org/W2163542565","https://openalex.org/W3047703793","https://openalex.org/W4211239749","https://openalex.org/W4294326239"],"related_works":["https://openalex.org/W2911386277","https://openalex.org/W2077318647","https://openalex.org/W2085998746","https://openalex.org/W1997944423","https://openalex.org/W2113966723","https://openalex.org/W2154338322","https://openalex.org/W2017236853","https://openalex.org/W1992633374","https://openalex.org/W2412156650","https://openalex.org/W2077675791"],"abstract_inverted_index":{"The":[0,72,169],"preferences":[1,141,175],"of":[2,39,52,87,164,194,218,225,239],"amino":[3,14,41,240],"acid":[4,241],"residues":[5,88,110,115],"for":[6,28,35,68,99,107,112,118,172,222],",psi":[7],"backbone":[8,20,70,140,174,178,190,206,219],"angles":[9],"vary":[10],"strikingly":[11,158],"among":[12],"the":[13,19,24,36,49,65,83,146,161,173,188,226,230],"acids,":[15],"as":[16,60],"shown":[17,55,214],"by":[18,56,130,183,192,215,234],"angle":[21],"found":[22],"from":[23,82,166],"(3)J(H(alpha),H(N))":[25,37],"coupling":[26,53,74,97],"constant":[27],"short":[29],"peptides":[30,58,101,155],"in":[31,90,94,135,153,160,187,210,229],"water.":[32],"New":[33],"data":[34],"values":[38,80,106],"blocked":[40],"acids":[42],"(dipeptides)":[43],"are":[44,76,127,142,157,180],"given":[45],"here.":[46],"Dipeptides":[47],"exhibit":[48],"full":[50],"range":[51],"constants":[54,75,98],"longer":[57],"such":[59],"GGXGG":[61,100,136,154],"and":[62,92,111,124,149,156,191,233],"dipeptides":[63],"present":[64],"simplest":[66,170],"system":[67],"analyzing":[69],"preferences.":[71],"dipeptide":[73,105,147,228],"surprisingly":[77],"close":[78],"to":[79],"computed":[81],"coil":[84,162],"library":[85,163],"(conformations":[86],"not":[89,93,117],"helices":[91],"sheets).":[95],"Published":[96],"agree":[102],"closely":[103],"with":[104,197],"all":[108],"nonpolar":[109],"some":[113],"polar":[114,131],"but":[116],"X":[119],"=":[120],"D,":[121],"N,":[122],"T,":[123],"Y,":[125],"which":[126,199],"probably":[128],"affected":[129,182],"side":[132,203],"chain-backbone":[133],"interactions":[134,186,196,208],"peptides.":[137],"Thus,":[138],"intrinsic":[139],"already":[143],"determined":[144],"at":[145],"level":[148],"remain":[150],"almost":[151],"unchanged":[152],"similar":[159],"conformations":[165,179],"protein":[167],"structures.":[168],"explanation":[171],"is":[176,213],"that":[177],"strongly":[181],"electrostatic":[184,207,220,235],"dipole-dipole":[185],"peptide":[189],"screening":[193],"these":[195],"water,":[198],"depends":[200],"on":[201],"nearby":[202],"chains.":[204],"Strong":[205],"occur":[209],"dipeptides.":[211,242],"This":[212],"calculations":[216],"both":[217],"energy":[221],"different":[223],"conformers":[224],"alanine":[227],"gas":[231],"phase":[232],"solvation":[236],"free":[237],"energies":[238]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":11}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}
