{"id":"https://openalex.org/W2895036336","doi":"https://doi.org/10.1021/acs.jcim.8b00592","title":"CRISPro: An Automated Pipeline for Protein Conformation Stabilization by Proline","display_name":"CRISPro: An Automated Pipeline for Protein Conformation Stabilization by Proline","publication_year":2018,"publication_date":"2018-10-05","ids":{"openalex":"https://openalex.org/W2895036336","doi":"https://doi.org/10.1021/acs.jcim.8b00592","mag":"2895036336","pmid":"https://pubmed.ncbi.nlm.nih.gov/30290119"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.8b00592","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00592","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/A5089740833","display_name":"Reda Rawi","orcid":"https://orcid.org/0000-0002-0445-2325"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reda Rawi","raw_affiliation_strings":["Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073226093","display_name":"Chen\u2010Hsiang Shen","orcid":"https://orcid.org/0000-0002-9560-3992"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chen-Hsiang Shen","raw_affiliation_strings":["Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043677118","display_name":"Peter D. Kwong","orcid":"https://orcid.org/0000-0003-3560-232X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter D. Kwong","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States","Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069049986","display_name":"Gwo\u2010Yu Chuang","orcid":"https://orcid.org/0000-0003-0375-1013"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gwo-Yu Chuang","raw_affiliation_strings":["Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States"],"raw_orcid":"https://orcid.org/0000-0003-0375-1013","affiliations":[{"raw_affiliation_string":"Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5069049986"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"],"apc_list":null,"apc_paid":null,"fwci":0.0931,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.48935097,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"58","issue":"11","first_page":"2189","last_page":"2192"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980000257492065,"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":0.9980000257492065,"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":0.994700014591217,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.983299970626831,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/pipeline","display_name":"Pipeline (software)","score":0.7641475200653076},{"id":"https://openalex.org/keywords/proline","display_name":"Proline","score":0.6903923749923706},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4549030065536499},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43801599740982056},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37742236256599426},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.30734360218048096},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.23554569482803345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19211792945861816},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06053689122200012}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7641475200653076},{"id":"https://openalex.org/C2779815552","wikidata":"https://www.wikidata.org/wiki/Q484583","display_name":"Proline","level":3,"score":0.6903923749923706},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4549030065536499},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43801599740982056},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37742236256599426},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.30734360218048096},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.23554569482803345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19211792945861816},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06053689122200012}],"mesh":[{"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":"D008958","descriptor_name":"Models, Molecular","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011392","descriptor_name":"Proline","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011392","descriptor_name":"Proline","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011392","descriptor_name":"Proline","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011392","descriptor_name":"Proline","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011392","descriptor_name":"Proline","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011392","descriptor_name":"Proline","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","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":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.8b00592","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00592","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:30290119","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30290119","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1968360645","https://openalex.org/W2001210310","https://openalex.org/W2008708467","https://openalex.org/W2040655728","https://openalex.org/W2109425369","https://openalex.org/W2126114330","https://openalex.org/W2131052727","https://openalex.org/W2138875004","https://openalex.org/W2154319440","https://openalex.org/W2162870223","https://openalex.org/W2178271040","https://openalex.org/W2750464792","https://openalex.org/W2767506818"],"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/W1532372971"],"abstract_inverted_index":{"Recent":[0],"studies":[1],"have":[2],"shown":[3],"that":[4,58,74,134],"the":[5,27,42,79,100],"yield,":[6],"antigenicity,":[7],"and":[8,86,111,125],"immunogenicity":[9],"of":[10,29,78,90,106,131],"an":[11,48,70,83],"immunogen":[12],"can":[13,59,116],"be":[14,117],"enhanced":[15],"by":[16],"stabilizing":[17],"it":[18],"into":[19,122],"a":[20,36,88,136],"specific":[21,123],"conformation.":[22,50],"Such":[23],"stabilization":[24],"often":[25],"involves":[26],"engineering":[28],"proline":[30,37,61,94],"mutations":[31,62,95],"at":[32],"residue":[33,91],"positions":[34,92],"where":[35,93],"is":[38,53],"structurally":[39],"compatible":[40],"with":[41,47],"target":[43,80,101,137],"conformation":[44,81,85,102,124],"but":[45],"not":[46],"alternative":[49,84],"However,":[51],"there":[52],"no":[54],"publicly":[55],"available":[56],"tool":[57],"design":[60,127],"for":[63],"this":[64],"purpose":[65],"automatically.":[66],"Here":[67],"we":[68],"implemented":[69],"automated":[71],"tool,":[72],"CRISPro,":[73],"inputs":[75],"structural":[76],"coordinates":[77],"and/or":[82],"outputs":[87],"list":[89],"are":[96],"predicted":[97],"to":[98,119,126],"stabilize":[99],"based":[103],"on":[104],"compatibility":[105],"phi-psi":[107],"angles,":[108],"secondary":[109],"structure,":[110],"steric":[112],"constraints.":[113],"Thus,":[114],"CRISPro":[115],"used":[118],"engineer":[120],"immunogens":[121],"serologic":[128],"probes,":[129],"capable":[130],"isolating":[132],"antibodies":[133],"recognize":[135],"shape.":[138]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
