{"id":"https://openalex.org/W2110530307","doi":"https://doi.org/10.1186/1471-2105-12-s12-s5","title":"Planning combinatorial disulfide cross-links for protein fold determination","display_name":"Planning combinatorial disulfide cross-links for protein fold determination","publication_year":2011,"publication_date":"2011-11-24","ids":{"openalex":"https://openalex.org/W2110530307","doi":"https://doi.org/10.1186/1471-2105-12-s12-s5","mag":"2110530307","pmid":"https://pubmed.ncbi.nlm.nih.gov/22168447"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-s12-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-s12-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S12-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S12-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050600154","display_name":"Fei Xiong","orcid":"https://orcid.org/0000-0002-3571-1772"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fei Xiong","raw_affiliation_strings":["Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA","[Department of Computer Science, Dartmouth College, Hanover, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA","institution_ids":["https://openalex.org/I107672454"]},{"raw_affiliation_string":"[Department of Computer Science, Dartmouth College, Hanover, USA]","institution_ids":["https://openalex.org/I107672454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088598434","display_name":"Alan M. Friedman","orcid":"https://orcid.org/0000-0002-5947-0950"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan M Friedman","raw_affiliation_strings":["Department of Biological Sciences, Markey Center for Structural Biology, Purdue Cancer Center, and Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA","Department of Biological Sciences, Markey Center for Structural Biology, Purdue Cancer Center, and Bindley Bioscience Center, Purdue University, West Lafayette, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Markey Center for Structural Biology, Purdue Cancer Center, and Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Department of Biological Sciences, Markey Center for Structural Biology, Purdue Cancer Center, and Bindley Bioscience Center, Purdue University, West Lafayette, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030579910","display_name":"Chris Bailey\u2010Kellogg","orcid":"https://orcid.org/0000-0003-1860-0912"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chris Bailey-Kellogg","raw_affiliation_strings":["Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA","[Department of Computer Science, Dartmouth College, Hanover, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA","institution_ids":["https://openalex.org/I107672454"]},{"raw_affiliation_string":"[Department of Computer Science, Dartmouth College, Hanover, USA]","institution_ids":["https://openalex.org/I107672454"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5030579910"],"corresponding_institution_ids":["https://openalex.org/I107672454"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1311,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53408429,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"S12","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9017000198364258,"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":0.9017000198364258,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0414000004529953,"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/T11162","display_name":"Enzyme Structure and Function","score":0.014999999664723873,"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/computer-science","display_name":"Computer science","score":0.6111617088317871},{"id":"https://openalex.org/keywords/fold","display_name":"Fold (higher-order function)","score":0.5378943681716919},{"id":"https://openalex.org/keywords/cross-validation","display_name":"Cross-validation","score":0.5140136480331421},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.5117690563201904},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4927361309528351},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4506535530090332},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4365842938423157},{"id":"https://openalex.org/keywords/naive-bayes-classifier","display_name":"Naive Bayes classifier","score":0.42598414421081543},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4201495051383972},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38492074608802795},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35214218497276306},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.27585649490356445},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14971566200256348}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6111617088317871},{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.5378943681716919},{"id":"https://openalex.org/C27181475","wikidata":"https://www.wikidata.org/wiki/Q541014","display_name":"Cross-validation","level":2,"score":0.5140136480331421},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.5117690563201904},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4927361309528351},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4506535530090332},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4365842938423157},{"id":"https://openalex.org/C52001869","wikidata":"https://www.wikidata.org/wiki/Q812530","display_name":"Naive Bayes classifier","level":3,"score":0.42598414421081543},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4201495051383972},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38492074608802795},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35214218497276306},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.27585649490356445},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14971566200256348},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","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":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-12-s12-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-s12-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S12-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22168447","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22168447","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:abff5c62d46c4c529a81a88c9a8ac56d","is_oa":false,"landing_page_url":"https://doaj.org/article/abff5c62d46c4c529a81a88c9a8ac56d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss Suppl 12, p S5 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2251634","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3247086","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-s12-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-s12-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S12-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4992483938","display_name":"AF:Small:Collaborative Research: Algorithmic Problems in Protein Structure Studies","funder_award_id":"0915388","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320335265","display_name":"Institute of Molecular and Cell Biology","ror":"https://ror.org/04xpsrn94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2110530307.pdf","grobid_xml":"https://content.openalex.org/works/W2110530307.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1523469746","https://openalex.org/W1570713908","https://openalex.org/W1982254415","https://openalex.org/W1989777815","https://openalex.org/W1995050941","https://openalex.org/W2008708467","https://openalex.org/W2012534919","https://openalex.org/W2019285341","https://openalex.org/W2020275421","https://openalex.org/W2023257869","https://openalex.org/W2027166643","https://openalex.org/W2073758233","https://openalex.org/W2091088808","https://openalex.org/W2108067237","https://openalex.org/W2112315506","https://openalex.org/W2112452502","https://openalex.org/W2153187042","https://openalex.org/W2154053567","https://openalex.org/W2157430275","https://openalex.org/W2160672912","https://openalex.org/W2168607352","https://openalex.org/W2324529874","https://openalex.org/W2416859981","https://openalex.org/W4241935390","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1181095405","https://openalex.org/W3014426369","https://openalex.org/W4240318783","https://openalex.org/W2311285072","https://openalex.org/W1573293794","https://openalex.org/W783636722","https://openalex.org/W2292230535","https://openalex.org/W2537862391","https://openalex.org/W2417174640","https://openalex.org/W2293349767"],"abstract_inverted_index":{"BACKGROUND:":[0],"Fold":[1,332],"recognition":[2,41,134,342],"techniques":[3],"take":[4],"advantage":[5],"of":[6,10,23,32,58,110,120,150,154,164,179,215,267,276,287,295,299,317],"the":[7,21,30,46,66,70,76,90,108,142,146,169,184,213,223,251,258,265,281,296,319,327],"limited":[8],"number":[9,275,298],"overall":[11,230],"structural":[12,128],"organizations,":[13],"and":[14,69,159,233,248,256],"have":[15,284],"become":[16],"increasingly":[17],"effective":[18],"at":[19],"identifying":[20],"fold":[22,40,109,133,241,341],"a":[24,50,56,111,118,137,161,172,177,205,217,274,292,313],"given":[25],"target":[26,112],"sequence.":[27],"However,":[28],"in":[29,148,250,257,270,338],"absence":[31],"sufficient":[33],"sequence":[34],"identity,":[35],"it":[36,62,116],"remains":[37],"difficult":[38],"for":[39,222,273],"methods":[42,82],"to":[43,87,106,182,195,211,237,246,323],"always":[44],"select":[45,160],"correct":[47,218,320],"model.":[48],"While":[49],"native-like":[51],"model":[52,71],"is":[53,63,244],"often":[54],"among":[55,89],"pool":[57],"highly":[59],"ranked":[60],"models,":[61],"not":[64],"necessarily":[65],"highest-ranked":[67],"one,":[68],"rankings":[72],"depend":[73],"sensitively":[74],"on":[75,93,229],"scoring":[77,336],"function":[78],"used.":[79],"Structure":[80],"elucidation":[81],"can":[83,334],"then":[84],"be":[85],"employed":[86],"decide":[88],"models":[91,129,147,252],"based":[92],"relatively":[94],"rapid":[95],"biochemical/biophysical":[96],"experiments.":[97],"RESULTS:":[98],"This":[99],"paper":[100],"presents":[101],"an":[102,191],"integrated":[103],"computational-experimental":[104],"method":[105],"determine":[107,176],"protein":[113,351],"by":[114,131],"probing":[115],"with":[117,126,204,305],"set":[119,163,178],"planned":[121],"disulfide":[122],"cross-links.":[123],"We":[124,263],"start":[125],"predicted":[127],"obtained":[130],"standard":[132],"techniques.":[135],"In":[136,171],"first":[138],"stage,":[139,174],"we":[140,175],"characterize":[141,212],"fold-level":[143],"differences":[144,232],"between":[145],"terms":[149],"topological":[151,231],"(contact)":[152],"patterns":[153],"secondary":[155],"structure":[156,260,352],"elements":[157],"(SSEs),":[158],"small":[162,293],"SSE":[165,186],"pairs":[166],"that":[167,280,310],"differentiate":[168],"folds.":[170],"second":[173],"residue-level":[180],"cross-links":[181,324],"probe":[183,238],"selected":[185],"pairs.":[187],"Each":[188],"stage":[189],"employs":[190],"information-theoretic":[192],"planning":[193,234],"algorithm":[194],"maximize":[196],"information":[197],"gain":[198],"while":[199,289,344],"minimizing":[200],"experimental":[201,347],"complexity,":[202],"along":[203],"Bayes":[206],"error":[207,288],"plan":[208,224],"assessment":[209],"framework":[210],"probability":[214],"making":[216],"decision":[219],"once":[220],"data":[221],"are":[225],"collected.":[226],"By":[227],"focusing":[228],"cross-linking":[235],"experiments":[236],"them,":[239],"our":[240,268],"determination":[242,333,353],"approach":[243,269],"robust":[245],"noise":[247],"uncertainty":[249],"(e.g.,":[253,261],"threading":[254],"misalignment)":[255],"actual":[259,328],"flexibility).":[262],"demonstrate":[264],"effectiveness":[266],"case":[271],"studies":[272,304],"CASP":[277],"targets,":[278],"showing":[279],"optimized":[282],"plans":[283,307],"low":[285],"risk":[286],"testing":[290],"only":[291],"portion":[294],"quadratic":[297],"possible":[300],"cross-link":[301],"candidates.":[302],"Simulation":[303],"these":[306],"further":[308],"show":[309],"they":[311],"do":[312],"very":[314],"good":[315],"job":[316],"selecting":[318],"model,":[321],"according":[322],"simulated":[325],"from":[326],"crystal":[329],"structures.":[330],"CONCLUSIONS:":[331],"overcome":[335],"limitations":[337],"purely":[339],"computational":[340],"methods,":[343],"requiring":[345],"less":[346],"effort":[348],"than":[349],"traditional":[350],"approaches.":[354]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}