{"id":"https://openalex.org/W1982120668","doi":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","title":"Construction of protein binding sites in scaffold structures","display_name":"Construction of protein binding sites in scaffold structures","publication_year":2000,"publication_date":"2000-01-01","ids":{"openalex":"https://openalex.org/W1982120668","doi":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","mag":"1982120668","pmid":"https://pubmed.ncbi.nlm.nih.gov/10984403"},"language":"en","primary_location":{"id":"doi:10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","doi":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","is_oa":false,"landing_page_url":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","pdf_url":null,"source":{"id":"https://openalex.org/S56808608","display_name":"Biopolymers","issn_l":"0006-3525","issn":["0006-3525","1097-0282"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biopolymers","raw_type":"journal-article"},"volume":null,"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/A5108381763","display_name":"Shide Liang","orcid":"https://orcid.org/0000-0003-2255-9887","observed_orcids":["https://orcid.org/0000-0003-2255-9887"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shide Liang","raw_affiliation_strings":["Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063368737","display_name":"Zhijie Liu","orcid":"https://orcid.org/0000-0003-1699-3468","observed_orcids":["https://orcid.org/0000-0003-1699-3468","https://orcid.org/0009-0003-6398-2427"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhijie Liu","raw_affiliation_strings":["Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027145422","display_name":"Weizhong Li","orcid":"https://orcid.org/0000-0003-1804-9403","observed_orcids":["https://orcid.org/0000-0003-1804-9403"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weizhong Li","raw_affiliation_strings":["Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008565692","display_name":"Lisheng Ni","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lisheng Ni","raw_affiliation_strings":["Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064049271","display_name":"Luhua Lai","orcid":"https://orcid.org/0000-0002-8343-7587","observed_orcids":["https://orcid.org/0000-0002-8343-7587"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Luhua Lai","raw_affiliation_strings":["Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, the People's Republic of China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064049271"],"corresponding_institution_ids":["https://openalex.org/I20231570"],"apc_list":{"value":4150,"currency":"USD","value_usd":4150},"apc_paid":null,"fwci":0.361,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.5518069,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"54","issue":"7","first_page":"515","last_page":"523"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9595000147819519,"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":0.9595000147819519,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.020500000566244125,"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/T11162","display_name":"Enzyme Structure and Function","score":0.008200000040233135,"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/protein-protein-interfaces","display_name":"protein-protein interfaces","score":0.7450000047683716},{"id":"https://openalex.org/keywords/scaffold-proteins","display_name":"scaffold proteins","score":0.8119999766349792},{"id":"https://openalex.org/keywords/barstar","display_name":"barstar","score":0.5199999809265137},{"id":"https://openalex.org/keywords/protein-protein-complex","display_name":"protein-protein complex","score":0.5189999938011169},{"id":"https://openalex.org/keywords/desolvation-energy","display_name":"desolvation energy","score":0.6840000152587891},{"id":"https://openalex.org/keywords/protein-protein-docking","display_name":"protein-protein docking","score":0.36000001430511475}],"concepts":[{"id":"https://openalex.org/C53645450","wikidata":"https://www.wikidata.org/wiki/Q907093","display_name":"Scaffold protein","level":3,"score":0.849087119102478},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.8027523756027222},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7186462879180908},{"id":"https://openalex.org/C2776559745","wikidata":"https://www.wikidata.org/wiki/Q4078377","display_name":"Barnase","level":5,"score":0.5720133781433105},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5386993288993835},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.47289860248565674},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.4523327350616455},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.44079458713531494},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.4368683695793152},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4304000735282898},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.41953369975090027},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.35169517993927},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.30242449045181274},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.14420053362846375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12044030427932739},{"id":"https://openalex.org/C136229726","wikidata":"https://www.wikidata.org/wiki/Q327092","display_name":"Biomedical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C2778976237","wikidata":"https://www.wikidata.org/wiki/Q422523","display_name":"Ribonuclease","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D001407","descriptor_name":"Bacillus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012260","descriptor_name":"Ribonucleases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012260","descriptor_name":"Ribonucleases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","doi":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","is_oa":false,"landing_page_url":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.0.co;2-0","pdf_url":null,"source":{"id":"https://openalex.org/S56808608","display_name":"Biopolymers","issn_l":"0006-3525","issn":["0006-3525","1097-0282"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biopolymers","raw_type":"journal-article"},{"id":"doi:10.1002/1097-0282(200012)54:7<515::aid-bip40>3.3.co;2-s","doi":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.3.co;2-s","is_oa":false,"landing_page_url":"https://doi.org/10.1002/1097-0282(200012)54:7<515::aid-bip40>3.3.co;2-s","pdf_url":null,"source":{"id":"https://openalex.org/S56808608","display_name":"Biopolymers","issn_l":"0006-3525","issn":["0006-3525","1097-0282"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biopolymers","raw_type":"journal-article"},{"id":"pmid:10984403","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/10984403","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":"Biopolymers","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1509956720","https://openalex.org/W1979650393","https://openalex.org/W1985724808","https://openalex.org/W1999727368","https://openalex.org/W2000383223","https://openalex.org/W2017212707","https://openalex.org/W2023003128","https://openalex.org/W2027978582","https://openalex.org/W2029198322","https://openalex.org/W2029377901","https://openalex.org/W2029762187","https://openalex.org/W2048362048","https://openalex.org/W2053475844","https://openalex.org/W2058527555","https://openalex.org/W2062351773","https://openalex.org/W2062819748","https://openalex.org/W2072948774","https://openalex.org/W2075097399","https://openalex.org/W2080796053","https://openalex.org/W2095805596","https://openalex.org/W2158408713","https://openalex.org/W2161711369","https://openalex.org/W2162166182","https://openalex.org/W2168890084","https://openalex.org/W2171356751","https://openalex.org/W4248357178"],"related_works":["https://openalex.org/W3145351929","https://openalex.org/W2161711369","https://openalex.org/W1987560617","https://openalex.org/W1516085465","https://openalex.org/W2007746130","https://openalex.org/W1979366468","https://openalex.org/W2804244900","https://openalex.org/W2315076298","https://openalex.org/W2136640709","https://openalex.org/W2106966628"],"abstract_inverted_index":{"We":[0],"have":[1,199],"developed":[2],"a":[3,7,17,24,39,165,200],"strategy":[4],"for":[5,87,176],"grafting":[6],"protein-protein":[8],"interface":[9,35,236],"based":[10,137],"on":[11],"the":[12,31,44,50,54,58,70,77,84,94,111,124,134,139,151,180,184,191,194,211,219,225,232,234,239],"known":[13],"crystal":[14],"structure":[15],"of":[16,89,141,183,237,241],"native":[18],"ligand":[19,32,59,71,112,125,135],"and":[20,67,157,170,196,228],"receptor":[21,51,78,152,158,197,226],"proteins":[22,159,163,198,250],"in":[23,53,69,110,123],"complex.":[25],"The":[26,128],"key":[27,65,107,120],"interaction":[28,108,121],"residues":[29,66,100,109,116,122],"at":[30],"protein":[33,41,47,52,86,126,130,136,186,221,227],"binding":[34,235],"are":[36,117,145,174,206,255],"transferred":[37],"onto":[38,133,245],"scaffold":[40,46,85,129,156,185,195,220,249],"so":[42,189],"that":[43,104,190],"mutated":[45,118],"will":[48],"bind":[49],"same":[55],"manner":[56],"as":[57],"protein.":[60,79,113,153],"First,":[61],"our":[62],"method":[63,82],"identifies":[64],"atoms":[68],"protein,":[72],"which":[73,93,144],"strongly":[74,148],"interact":[75,149],"with":[76,150,164,224,251],"Second,":[80],"this":[81],"searches":[83],"combinations":[88],"candidate":[90,99,115],"residues,":[91],"among":[92],"distance":[95],"between":[96,105,155,193],"any":[97],"two":[98],"is":[101,131,160,187,222],"similar":[102],"to":[103,119,147,209],"relevant":[106],"These":[114],"respectively.":[127],"superposed":[132],"upon":[138],"coordinates":[140],"corresponding":[142],"atoms,":[143],"assumed":[146],"Complementarity":[154],"evaluated.":[161,229],"Scaffold":[162],"low":[166],"superposing":[167],"rms":[168],"difference":[169],"high":[171,252],"complementary":[172,253],"score":[173],"accepted":[175],"further":[177],"analysis.":[178],"Then,":[179],"relative":[181],"position":[182],"adjusted":[188],"interfaces":[192],"reasonable":[201],"packing":[202],"density.":[203],"Other":[204],"mutations":[205],"also":[207],"considered":[208],"reduce":[210],"desolvation":[212],"energy":[213],"or":[214],"bad":[215],"steric":[216],"contacts.":[217],"Finally,":[218],"cominimized":[223],"To":[230],"test":[231],"method,":[233],"barstar,":[238],"inhibitor":[240],"barnase,":[242],"was":[243],"grafted":[244],"small":[246],"proteins.":[247],"Four":[248],"scores":[254],"accepted.":[256]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
