{"id":"https://openalex.org/W4226077530","doi":"https://doi.org/10.1021/acs.jcim.1c01406","title":"Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein\u2013Ligand Interaction Research","display_name":"Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein\u2013Ligand Interaction Research","publication_year":2022,"publication_date":"2022-03-29","ids":{"openalex":"https://openalex.org/W4226077530","doi":"https://doi.org/10.1021/acs.jcim.1c01406","pmid":"https://pubmed.ncbi.nlm.nih.gov/35347980"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c01406","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01406","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/A5060551318","display_name":"Kang Ding","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kang Ding","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046861536","display_name":"Shiqiu Yin","orcid":"https://orcid.org/0000-0001-8125-0367"},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiqiu Yin","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100726884","display_name":"Zhongwei Li","orcid":"https://orcid.org/0000-0003-1014-4238"},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhongwei Li","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017383460","display_name":"Shiju Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiju Jiang","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104037057","display_name":"Yang Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Yang","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100524959","display_name":"Wenbiao Zhou","orcid":"https://orcid.org/0000-0002-7168-3676"},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wenbiao Zhou","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070861971","display_name":"Yingsheng Zhang","orcid":"https://orcid.org/0000-0003-2520-3923"},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yingsheng Zhang","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101747154","display_name":"Bo Huang","orcid":"https://orcid.org/0000-0003-3822-9110"},"institutions":[{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bo Huang","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China"],"raw_orcid":"https://orcid.org/0000-0003-3822-9110","affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210161752"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100524959","https://openalex.org/A5101747154"],"corresponding_institution_ids":["https://openalex.org/I4210161752"],"apc_list":null,"apc_paid":null,"fwci":6.5066,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.97000122,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"62","issue":"7","first_page":"1734","last_page":"1743"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical 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/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6592106223106384},{"id":"https://openalex.org/keywords/macromolecule","display_name":"Macromolecule","score":0.6051816940307617},{"id":"https://openalex.org/keywords/intermolecular-force","display_name":"Intermolecular force","score":0.5769330859184265},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5223327875137329},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4992237091064453},{"id":"https://openalex.org/keywords/non-covalent-interactions","display_name":"Non-covalent interactions","score":0.4495670199394226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35827457904815674},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3325392007827759},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2459900677204132},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15094685554504395},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.12295818328857422},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09564119577407837},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.06689885258674622},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.0644940733909607}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6592106223106384},{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.6051816940307617},{"id":"https://openalex.org/C166950319","wikidata":"https://www.wikidata.org/wiki/Q245031","display_name":"Intermolecular force","level":3,"score":0.5769330859184265},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5223327875137329},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4992237091064453},{"id":"https://openalex.org/C137277065","wikidata":"https://www.wikidata.org/wiki/Q2915446","display_name":"Non-covalent interactions","level":4,"score":0.4495670199394226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35827457904815674},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3325392007827759},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2459900677204132},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15094685554504395},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.12295818328857422},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09564119577407837},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.06689885258674622},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0644940733909607}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","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":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c01406","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01406","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:35347980","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35347980","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":[{"id":"https://openalex.org/G3971797808","display_name":null,"funder_award_id":"Z211100003521001","funder_id":"https://openalex.org/F4320325902","funder_display_name":"Beijing Municipal Science and Technology Commission"}],"funders":[{"id":"https://openalex.org/F4320325902","display_name":"Beijing Municipal Science and Technology Commission","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1518170439","https://openalex.org/W2005212066","https://openalex.org/W2011301426","https://openalex.org/W2039839635","https://openalex.org/W2048011433","https://openalex.org/W2064142965","https://openalex.org/W2104919283","https://openalex.org/W2111762125","https://openalex.org/W2128983966","https://openalex.org/W2131417105","https://openalex.org/W2139779008","https://openalex.org/W2142257792","https://openalex.org/W2157998141","https://openalex.org/W2161239029","https://openalex.org/W2313176581","https://openalex.org/W2314431251","https://openalex.org/W2342249984","https://openalex.org/W2517767579","https://openalex.org/W2559438165","https://openalex.org/W2587598315","https://openalex.org/W2612329522","https://openalex.org/W2790403032","https://openalex.org/W2793821032","https://openalex.org/W2911997094","https://openalex.org/W2945542316","https://openalex.org/W2958873833","https://openalex.org/W2973457155","https://openalex.org/W2985871121","https://openalex.org/W3009761974","https://openalex.org/W3011505309","https://openalex.org/W3035965352","https://openalex.org/W3048472708","https://openalex.org/W3085817819","https://openalex.org/W3099878876","https://openalex.org/W3120951562","https://openalex.org/W3185227028"],"related_works":["https://openalex.org/W2315830929","https://openalex.org/W4306790628","https://openalex.org/W3161599862","https://openalex.org/W3214657337","https://openalex.org/W4312114024","https://openalex.org/W2072096999","https://openalex.org/W1485106526","https://openalex.org/W1964211192","https://openalex.org/W4400523916","https://openalex.org/W3008230527"],"abstract_inverted_index":{"We":[0,47,69],"report":[1],"for":[2,18,24,98,119],"the":[3,6,14,72,75,78,90,113],"first":[4,45],"time":[5],"use":[7],"of":[8,20,74,80,115],"experimental":[9],"electron":[10,33],"density":[11,34],"(ED)":[12],"in":[13,77,84],"Protein":[15],"Data":[16],"Bank":[17],"modeling":[19],"noncovalent":[21],"interactions":[22,83],"(NCIs)":[23],"protein-ligand":[25,67,85,99,120],"complexes.":[26,68],"Our":[27],"methodology":[28],"is":[29],"based":[30],"on":[31,94,108],"reduced":[32],"gradient":[35],"(RDG)":[36],"theory":[37],"describing":[38],"intermolecular":[39],"NCIs":[40,63,97,111],"by":[41],"ED":[42,58],"and":[43,101,112],"its":[44],"derivative.":[46],"established":[48],"a":[49],"database":[50,76,91],"named":[51],"Experimental":[52],"NCI":[53],"Database":[54],"(ExptNCI;":[55],"http://ncidatabase.stonewise.cn/#/nci)":[56],"containing":[57],"saddle":[59],"points,":[60],"indicating":[61],"\u223c200,000":[62],"from":[64],"over":[65],"12,000":[66],"also":[70],"demonstrated":[71],"usage":[73],"case":[79],"depicting":[81],"amide-\u03c0":[82],"binding":[86,121],"systems.":[87],"In":[88],"summary,":[89],"provides":[92],"details":[93],"experimentally":[95],"observed":[96],"complexes":[100],"can":[102],"support":[103],"future":[104],"studies":[105,107],"including":[106],"rarely":[109],"documented":[110],"development":[114],"artificial":[116],"intelligence":[117],"models":[118],"prediction.":[122]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
