{"id":"https://openalex.org/W7155106409","doi":"https://doi.org/10.1142/s0219720026710010","title":"Bond-resolved graph-theoretic modeling of structural invariance and metabolic accessibility in drug molecules","display_name":"Bond-resolved graph-theoretic modeling of structural invariance and metabolic accessibility in drug molecules","publication_year":2026,"publication_date":"2026-04-01","ids":{"openalex":"https://openalex.org/W7155106409","doi":"https://doi.org/10.1142/s0219720026710010","pmid":"https://pubmed.ncbi.nlm.nih.gov/42011126"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720026710010","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720026710010","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5134199138","display_name":"K. Nalini Devi","orcid":"https://orcid.org/0009-0006-8989-5462"},"institutions":[{"id":"https://openalex.org/I2802584695","display_name":"Government of Karnataka","ror":"https://ror.org/00maf9573","country_code":"IN","type":"government","lineage":["https://openalex.org/I2802584695"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"K. Nalini Devi","raw_affiliation_strings":["Department of Mathematics, Government First Grade College, K. R. Pura, Bangalore 560036, Karnataka, India"],"raw_orcid":"https://orcid.org/0009-0006-8989-5462","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Government First Grade College, K. R. Pura, Bangalore 560036, Karnataka, India","institution_ids":["https://openalex.org/I2802584695"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112494133","display_name":"G. Srinivasa","orcid":null},"institutions":[{"id":"https://openalex.org/I2800071334","display_name":"Horizon College and Seminary","ror":"https://ror.org/01sjjfh02","country_code":"CA","type":"education","lineage":["https://openalex.org/I2800071334","https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"G. Srinivasa","raw_affiliation_strings":["Department of Mathematics, New Horizon College of Engineering, Bengaluru 560103, Karnataka, India"],"raw_orcid":"https://orcid.org/0000-0003-0315-9423","affiliations":[{"raw_affiliation_string":"Department of Mathematics, New Horizon College of Engineering, Bengaluru 560103, Karnataka, India","institution_ids":["https://openalex.org/I2800071334"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.35067538,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"24","issue":"02","first_page":"2671001","last_page":"2671001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.24480000138282776,"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":0.24480000138282776,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.22439999878406525,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.19050000607967377,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6238999962806702},{"id":"https://openalex.org/keywords/invariant","display_name":"Invariant (physics)","score":0.5077000260353088},{"id":"https://openalex.org/keywords/steric-effects","display_name":"Steric effects","score":0.4966999888420105},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.45399999618530273},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.359499990940094},{"id":"https://openalex.org/keywords/cuboid","display_name":"Cuboid","score":0.3109000027179718},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.310699999332428},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.30550000071525574}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6238999962806702},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.5077000260353088},{"id":"https://openalex.org/C201194858","wikidata":"https://www.wikidata.org/wiki/Q898238","display_name":"Steric effects","level":2,"score":0.4966999888420105},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.45399999618530273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4320000112056732},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4072999954223633},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3856000006198883},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.38109999895095825},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.359499990940094},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.31850001215934753},{"id":"https://openalex.org/C203527163","wikidata":"https://www.wikidata.org/wiki/Q262959","display_name":"Cuboid","level":2,"score":0.3109000027179718},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.310699999332428},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.30550000071525574},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.2994000017642975},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.2957000136375427},{"id":"https://openalex.org/C206175624","wikidata":"https://www.wikidata.org/wiki/Q595731","display_name":"Branching (polymer chemistry)","level":2,"score":0.2874999940395355},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.28200000524520874},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.27799999713897705},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2777999937534332},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2766000032424927},{"id":"https://openalex.org/C64999384","wikidata":"https://www.wikidata.org/wiki/Q3507967","display_name":"Symmetrization","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.273499995470047},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.2700999975204468},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.2662000060081482},{"id":"https://openalex.org/C130367717","wikidata":"https://www.wikidata.org/wiki/Q189791","display_name":"Diagonal","level":2,"score":0.25189998745918274},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.251800000667572},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.2517000138759613},{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.25040000677108765}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720026710010","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720026710010","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:42011126","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42011126","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 bioinformatics and computational biology","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.4903809130191803,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2010427019","https://openalex.org/W2033757486","https://openalex.org/W2113524447","https://openalex.org/W2137608611","https://openalex.org/W2160317546","https://openalex.org/W2952997412"],"related_works":[],"abstract_inverted_index":{"In":[0],"this":[1,144],"paper,":[2],"we":[3,75],"develop":[4],"a":[5,19,22,35,43,81,131,139,151,164],"connectivity-exact":[6],"bond-resolved":[7],"framework":[8,145],"for":[9],"quantifying":[10],"structural":[11,112,170],"accessibility":[12,171],"and":[13,88,114,172],"persistence":[14,147],"in":[15,118],"drug":[16],"molecules.":[17],"Representing":[18],"molecule":[20],"as":[21,33,126,150],"heavy-atom":[23],"graph":[24,157],"[Formula:":[25,54,95,102],"see":[26,40,48,55,96,103],"text]":[27,56,104],"each":[28],"bond":[29,38,46,120],"is":[30,124,148],"classified":[31],"uniquely":[32],"either":[34],"connectivity-critical":[36],"Entry-point":[37],"([Formula:":[39,47],"text])":[41,49],"or":[42],"connectivity-preserving":[44],"Fortress":[45],"yielding":[50],"the":[51,72,135],"exact":[52],"identity":[53],"This":[57],"exhaustive":[58],"partition":[59],"separates":[60],"fragmentation":[61],"capacity":[62],"from":[63,109],"invariant":[64],"scaffold":[65,146],"structure":[66],"without":[67],"adjustable":[68],"parameters.":[69],"To":[70],"refine":[71],"invariance":[73],"coordinate":[74],"introduce":[76],"Total":[77],"Structural":[78],"Entrenchment":[79],"(TSE)":[80],"persistence-weighted":[82],"functional":[83],"defined":[84],"over":[85],"cycle-supported":[86],"bonds":[87],"modulated":[89],"by":[90,156],"local":[91],"steric":[92],"wall":[93],"contributions":[94],"text].":[97],"The":[98,159],"resulting":[99,160],"two-parameter":[100],"embedding":[101,162],"distinguishes":[105],"superficial":[106],"cyclic":[107,173],"extent":[108],"deeply":[110],"embedded":[111],"reinforcement":[113],"resolves":[115],"degeneracies":[116],"inherent":[117],"raw":[119],"counts.":[121],"Metabolic":[122],"progression":[123],"formalized":[125],"recursive":[127],"bridge":[128],"depletion":[129],"generating":[130],"directed":[132],"migration":[133],"across":[134],"architectural":[136],"plane":[137],"toward":[138],"bridge-depleted":[140],"refractory":[141],"core.":[142],"Within":[143],"interpreted":[149],"connectivity-driven":[152],"contraction":[153],"governed":[154],"strictly":[155],"topology.":[158],"invariance-variation":[161],"establishes":[163],"mathematically":[165],"controlled":[166],"bond-level":[167],"representation":[168],"of":[169],"entrenchment.":[174]},"counts_by_year":[],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2026-04-22T00:00:00"}
