{"id":"https://openalex.org/W4385603245","doi":"https://doi.org/10.1007/s10822-023-00526-0","title":"Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations","display_name":"Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations","publication_year":2023,"publication_date":"2023-08-05","ids":{"openalex":"https://openalex.org/W4385603245","doi":"https://doi.org/10.1007/s10822-023-00526-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/37542610"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-023-00526-0","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-023-00526-0","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5044043619","display_name":"J Singh","orcid":"https://orcid.org/0000-0003-0850-0950"},"institutions":[{"id":"https://openalex.org/I73779912","display_name":"Manipal University Jaipur","ror":"https://ror.org/040h76494","country_code":null,"type":"education","lineage":["https://openalex.org/I73779912"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Jaikee Kumar Singh","raw_affiliation_strings":["Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India","institution_ids":["https://openalex.org/I73779912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023561639","display_name":"Jai Prakash Singh","orcid":"https://orcid.org/0000-0003-3601-1126"},"institutions":[{"id":"https://openalex.org/I73779912","display_name":"Manipal University Jaipur","ror":"https://ror.org/040h76494","country_code":null,"type":"education","lineage":["https://openalex.org/I73779912"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Jai Singh","raw_affiliation_strings":["Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India","institution_ids":["https://openalex.org/I73779912"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100711155","display_name":"Sandeep Kumar Srivastava","orcid":"https://orcid.org/0000-0002-7138-1387"},"institutions":[{"id":"https://openalex.org/I4210165321","display_name":"Manipal Hospital","ror":"https://ror.org/05mryn396","country_code":"IN","type":"healthcare","lineage":["https://openalex.org/I4210165321"]},{"id":"https://openalex.org/I73779912","display_name":"Manipal University Jaipur","ror":"https://ror.org/040h76494","country_code":null,"type":"education","lineage":["https://openalex.org/I73779912"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Sandeep Kumar Srivastava","raw_affiliation_strings":["Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India. sandeepkumar.srivastava@jaipur.manipal.edu","Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India. sandeepkumar.srivastava@jaipur.manipal.edu","institution_ids":["https://openalex.org/I4210165321"]},{"raw_affiliation_string":"Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India","institution_ids":["https://openalex.org/I73779912"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100711155"],"corresponding_institution_ids":["https://openalex.org/I4210165321","https://openalex.org/I73779912"],"apc_list":{"value":3690,"currency":"USD","value_usd":3690},"apc_paid":null,"fwci":0.4645,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58249457,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"37","issue":"11","first_page":"551","last_page":"563"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9968000054359436,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9968000054359436,"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/T12477","display_name":"Toxin Mechanisms and Immunotoxins","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6523815393447876},{"id":"https://openalex.org/keywords/static-electricity","display_name":"Static electricity","score":0.5308723449707031},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.4969678223133087},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.49604830145835876},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.4644045829772949},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.458692729473114},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4545019567012787},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4290359318256378},{"id":"https://openalex.org/keywords/epistasis","display_name":"Epistasis","score":0.410045325756073},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.347720742225647},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29275208711624146},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22441443800926208},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14731529355049133},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.14278742671012878}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6523815393447876},{"id":"https://openalex.org/C87716614","wikidata":"https://www.wikidata.org/wiki/Q845744","display_name":"Static electricity","level":2,"score":0.5308723449707031},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.4969678223133087},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.49604830145835876},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.4644045829772949},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.458692729473114},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4545019567012787},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4290359318256378},{"id":"https://openalex.org/C61727976","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Epistasis","level":3,"score":0.410045325756073},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.347720742225647},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29275208711624146},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22441443800926208},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14731529355049133},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.14278742671012878},{"id":"https://openalex.org/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"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":"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":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-023-00526-0","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-023-00526-0","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:37542610","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37542610","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 computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8999999761581421,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G499876932","display_name":null,"funder_award_id":"CRG/2020/002008","funder_id":"https://openalex.org/F4320334771","funder_display_name":"Science and Engineering Research Board"}],"funders":[{"id":"https://openalex.org/F4320334771","display_name":"Science and Engineering Research Board","ror":"https://ror.org/03ffdsr55"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1969017401","https://openalex.org/W2021520922","https://openalex.org/W2029667189","https://openalex.org/W2044172327","https://openalex.org/W2048740445","https://openalex.org/W2067174909","https://openalex.org/W2074473216","https://openalex.org/W2075828031","https://openalex.org/W2125304058","https://openalex.org/W2128572087","https://openalex.org/W2132629607","https://openalex.org/W2266013672","https://openalex.org/W2555870966","https://openalex.org/W2623296956","https://openalex.org/W2751476102","https://openalex.org/W2913977622","https://openalex.org/W3023376619","https://openalex.org/W3095150813","https://openalex.org/W3159657574","https://openalex.org/W3217650782","https://openalex.org/W4206737621","https://openalex.org/W4281939105","https://openalex.org/W4283159267","https://openalex.org/W4283319609","https://openalex.org/W4283831060","https://openalex.org/W4285729774","https://openalex.org/W4311359167","https://openalex.org/W4313533812","https://openalex.org/W4313887879","https://openalex.org/W4318683801","https://openalex.org/W4318775173","https://openalex.org/W4319066889","https://openalex.org/W4324355415","https://openalex.org/W4360862839"],"related_works":["https://openalex.org/W1547817677","https://openalex.org/W2023460495","https://openalex.org/W2615678788","https://openalex.org/W1967902778","https://openalex.org/W3083099115","https://openalex.org/W1981509636","https://openalex.org/W4235217192","https://openalex.org/W3139253026","https://openalex.org/W3035525216","https://openalex.org/W2029152669"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
