{"id":"https://openalex.org/W4408841779","doi":"https://doi.org/10.3389/fbinf.2025.1535482","title":"Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment","display_name":"Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment","publication_year":2025,"publication_date":"2025-03-26","ids":{"openalex":"https://openalex.org/W4408841779","doi":"https://doi.org/10.3389/fbinf.2025.1535482","pmid":"https://pubmed.ncbi.nlm.nih.gov/40206634"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1535482","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1535482","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1535482/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1535482/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109109739","display_name":"Samina Malik","orcid":"https://orcid.org/0000-0002-3410-6378"},"institutions":[{"id":"https://openalex.org/I142204992","display_name":"University of Lahore","ror":"https://ror.org/051jrjw38","country_code":"PK","type":"education","lineage":["https://openalex.org/I142204992"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Samina Malik","raw_affiliation_strings":["University College of Medicine and Dentistry, The University of Lahore, IMBB, UOL, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University College of Medicine and Dentistry, The University of Lahore, IMBB, UOL, Lahore, Pakistan","institution_ids":["https://openalex.org/I142204992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039607420","display_name":"Mirza Jawad ul Hasnain","orcid":"https://orcid.org/0000-0002-4949-8060"},"institutions":[{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]},{"id":"https://openalex.org/I79571142","display_name":"Virtual University of Pakistan","ror":"https://ror.org/00ya1zd25","country_code":"PK","type":"education","lineage":["https://openalex.org/I79571142"]}],"countries":["CN","PK"],"is_corresponding":false,"raw_author_name":"Mirza Jawad Ul Hasnain","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China","Department of Biological Sciences, Virtual University of Pakistan, Islamabad, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Department of Biological Sciences, Virtual University of Pakistan, Islamabad, Pakistan","institution_ids":["https://openalex.org/I79571142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107543382","display_name":"Gul Zaib","orcid":null},"institutions":[{"id":"https://openalex.org/I142204992","display_name":"University of Lahore","ror":"https://ror.org/051jrjw38","country_code":"PK","type":"education","lineage":["https://openalex.org/I142204992"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Gul Zaib","raw_affiliation_strings":["School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan","institution_ids":["https://openalex.org/I142204992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035074906","display_name":"Haleema Saadia","orcid":"https://orcid.org/0009-0008-4498-9005"},"institutions":[{"id":"https://openalex.org/I142204992","display_name":"University of Lahore","ror":"https://ror.org/051jrjw38","country_code":"PK","type":"education","lineage":["https://openalex.org/I142204992"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Haleema Saadia","raw_affiliation_strings":["School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan","institution_ids":["https://openalex.org/I142204992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051384303","display_name":"Arif Malik","orcid":"https://orcid.org/0000-0002-1894-6772"},"institutions":[{"id":"https://openalex.org/I142204992","display_name":"University of Lahore","ror":"https://ror.org/051jrjw38","country_code":"PK","type":"education","lineage":["https://openalex.org/I142204992"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Arif Malik","raw_affiliation_strings":["School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan","institution_ids":["https://openalex.org/I142204992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051676936","display_name":"Ayesha Zahid","orcid":"https://orcid.org/0000-0003-3427-984X"},"institutions":[{"id":"https://openalex.org/I142204992","display_name":"University of Lahore","ror":"https://ror.org/051jrjw38","country_code":"PK","type":"education","lineage":["https://openalex.org/I142204992"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Ayesha Zahid","raw_affiliation_strings":["School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pain and Regenerative Medicine, The University of Lahore, IMBB, UOL, Lahore, Pakistan","institution_ids":["https://openalex.org/I142204992"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5051384303"],"corresponding_institution_ids":["https://openalex.org/I142204992"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.4868,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.60931206,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"5","issue":null,"first_page":"1535482","last_page":"1535482"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.6862999796867371,"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/T10123","display_name":"DNA Repair Mechanisms","score":0.6862999796867371,"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/T11914","display_name":"PARP inhibition in cancer therapy","score":0.0714000016450882,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11369","display_name":"Genetic factors in colorectal cancer","score":0.05990000069141388,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"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/rad50","display_name":"Rad50","score":0.8528307676315308},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5528021454811096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5435053110122681},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.505924642086029},{"id":"https://openalex.org/keywords/dna-repair","display_name":"DNA repair","score":0.4774359166622162},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44885939359664917},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.42250487208366394},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.21835994720458984},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.07331553101539612}],"concepts":[{"id":"https://openalex.org/C2775984157","wikidata":"https://www.wikidata.org/wiki/Q18035037","display_name":"Rad50","level":5,"score":0.8528307676315308},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5528021454811096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5435053110122681},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.505924642086029},{"id":"https://openalex.org/C134935766","wikidata":"https://www.wikidata.org/wiki/Q210538","display_name":"DNA repair","level":3,"score":0.4774359166622162},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44885939359664917},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.42250487208366394},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.21835994720458984},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.07331553101539612}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1535482","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1535482","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1535482/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40206634","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40206634","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:852769de27b14aa986cf57bcd63aac4e","is_oa":true,"landing_page_url":"https://doaj.org/article/852769de27b14aa986cf57bcd63aac4e","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11979129","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11979129","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1535482","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1535482","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1535482/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.6800000071525574,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408841779.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1563940013","https://openalex.org/W1789533439","https://openalex.org/W1964957202","https://openalex.org/W1987134040","https://openalex.org/W2002052142","https://openalex.org/W2009239521","https://openalex.org/W2012607520","https://openalex.org/W2023350260","https://openalex.org/W2052156860","https://openalex.org/W2053538195","https://openalex.org/W2059287705","https://openalex.org/W2115152262","https://openalex.org/W2121519777","https://openalex.org/W2137886330","https://openalex.org/W2170060741","https://openalex.org/W2376573086","https://openalex.org/W2414667422","https://openalex.org/W2606462312","https://openalex.org/W2612969216","https://openalex.org/W2890841681","https://openalex.org/W2905452503","https://openalex.org/W2912175037","https://openalex.org/W2968494487","https://openalex.org/W2990895669","https://openalex.org/W3013636475","https://openalex.org/W3087805512","https://openalex.org/W3110917833","https://openalex.org/W3113552956","https://openalex.org/W3125103249","https://openalex.org/W3177914501","https://openalex.org/W3195375135","https://openalex.org/W3209435229","https://openalex.org/W3212854871","https://openalex.org/W3214317312","https://openalex.org/W4200375412","https://openalex.org/W4307635107","https://openalex.org/W4360986151","https://openalex.org/W4366996323","https://openalex.org/W4385741267","https://openalex.org/W4386861232","https://openalex.org/W6850623069"],"related_works":["https://openalex.org/W2312186357","https://openalex.org/W2155835698","https://openalex.org/W2034103052","https://openalex.org/W2112005097","https://openalex.org/W3125103249","https://openalex.org/W4319017166","https://openalex.org/W2037519090","https://openalex.org/W4387397534","https://openalex.org/W4388589230","https://openalex.org/W2049118227"],"abstract_inverted_index":{"Background:":[0],"The":[1,126,207],"RAD50":[2,47,169,214,229],"gene":[3,170],"on":[4,54,57,95,141,216],"chromosome":[5],"5q3.11":[6],"plays":[7],"an":[8],"important":[9],"role":[10,152],"in":[11,46,155,167,183],"the":[12,22,38,63,105,137,151,168,172,178,184,210,217,225],"MRN":[13,64],"(Mre11-Rad50-Nbs1)":[14],"complex.":[15,65],"This":[16,33],"complex":[17],"orchestrates":[18],"cellular":[19],"responses":[20],"to":[21,36,76,135,149,227],"DNA":[23,200],"double-strand":[24],"breaks":[25],"(DSBs)":[26],"through":[27],"several":[28],"pathways":[29],"for":[30,104,111,122,199],"genome":[31,204],"stability.":[32,205],"study":[34,208],"aims":[35],"investigate":[37],"functional":[39],"impact":[40,138,212],"of":[41,69,82,128,139,153,162,187,213,219],"non-synonymous":[42],"single-nucleotide":[43],"polymorphisms":[44],"(nsSNPs)":[45],"(a":[48],"breast":[49,220],"cancer-associated":[50],"gene)":[51],"and":[52,60,74,85,88,118,164,175,194,203],"focuses":[53],"their":[55],"consequences":[56],"protein":[58,89,123,173],"structure":[59,113,124],"interaction":[61],"within":[62],"Methods:":[66],"A":[67,160],"total":[68],"1,806":[70],"nsSNPs":[71,101,140,166],"were":[72,92,102,120],"retrieved":[73],"subjected":[75],"variant":[77],"analysis":[78],"using":[79,133],"a":[80],"set":[81],"computational":[83],"tools":[84],"ConSurf.":[86],"Pathogenicity":[87],"stability":[90,174],"criteria":[91],"established":[93],"based":[94],"specific":[96],"tools.":[97],"Highly":[98],"conserved":[99],"damaging":[100],"prioritized":[103],"structural":[106],"analysis.":[107,158],"GOR-IV":[108],"was":[109,131,147],"used":[110,121],"secondary":[112],"prediction,":[114],"whereas":[115],"AlphaFold,":[116],"RoseTTAFold,":[117],"I-TASSER":[119],"prediction.":[125],"docking":[127,157],"RAD50-Mre11A":[129],"complexes":[130],"performed":[132,148],"HADDOCK":[134],"assess":[136],"protein-protein":[142],"interactions.":[143],"Molecular":[144],"dynamic":[145],"simulation":[146],"verify":[150],"mutants":[154,188],"molecular":[156],"Results:":[159],"subset":[161],"pathogenic":[163],"disease-associated":[165],"altered":[171],"interactions":[176],"with":[177],"Mre11A":[179],"protein.":[180],"Substantial":[181],"alterations":[182],"interacting":[185],"profiles":[186],"(A73P,":[189],"V117F,":[190],"L518P,":[191],"L1092R,":[192],"N1144S,":[193],"A1209T)":[195],"suggest":[196],"potential":[197],"implications":[198],"repair":[201],"mechanisms":[202],"Conclusion:":[206],"discloses":[209],"normative":[211],"mutations":[215],"pathophysiology":[218],"cancer.":[221],"It":[222],"can":[223],"provide":[224],"basis":[226],"treat":[228],"mutation-deficient":[230],"cells.":[231]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
