{"id":"https://openalex.org/W4417248866","doi":"https://doi.org/10.1109/tvcg.2025.3634636","title":"BondMatcher: H-Bond Stability Analysis in Molecular Systems","display_name":"BondMatcher: H-Bond Stability Analysis in Molecular Systems","publication_year":2025,"publication_date":"2025-12-11","ids":{"openalex":"https://openalex.org/W4417248866","doi":"https://doi.org/10.1109/tvcg.2025.3634636","pmid":"https://pubmed.ncbi.nlm.nih.gov/41379924"},"language":"en","primary_location":{"id":"doi:10.1109/tvcg.2025.3634636","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2025.3634636","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","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/A5103069356","display_name":"Thomas Daniel","orcid":"https://orcid.org/0000-0002-2627-3686"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I182627622","display_name":"Universit\u00e9 Sorbonne Nouvelle","ror":"https://ror.org/03z6jp965","country_code":"FR","type":"education","lineage":["https://openalex.org/I182627622"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I51101395","display_name":"Universit\u00e9 Paris 1 Panth\u00e9on-Sorbonne","ror":"https://ror.org/002t25c44","country_code":"FR","type":"education","lineage":["https://openalex.org/I51101395"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Thomas Daniel","raw_affiliation_strings":["CNRS and Sorbonne University, France","CNRS, Sorbonne France University, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS and Sorbonne University, France","institution_ids":["https://openalex.org/I39804081","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"CNRS, Sorbonne France University, France","institution_ids":["https://openalex.org/I182627622","https://openalex.org/I51101395","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024806992","display_name":"Ma\u0142gorzata Olejniczak","orcid":"https://orcid.org/0000-0002-8370-9570"},"institutions":[{"id":"https://openalex.org/I4210133331","display_name":"AM Technologies (Poland)","ror":"https://ror.org/03jpvv707","country_code":"PL","type":"company","lineage":["https://openalex.org/I4210133331"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Malgorzata Olejniczak","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw, Poland","Centre of New Technologies, the University of Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Centre of New Technologies, the University of Warsaw, Poland","institution_ids":["https://openalex.org/I4210133331"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074734666","display_name":"Julien Tierny","orcid":"https://orcid.org/0000-0003-0056-2831"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I182627622","display_name":"Universit\u00e9 Sorbonne Nouvelle","ror":"https://ror.org/03z6jp965","country_code":"FR","type":"education","lineage":["https://openalex.org/I182627622"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I51101395","display_name":"Universit\u00e9 Paris 1 Panth\u00e9on-Sorbonne","ror":"https://ror.org/002t25c44","country_code":"FR","type":"education","lineage":["https://openalex.org/I51101395"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Julien Tierny","raw_affiliation_strings":["CNRS and Sorbonne University, France","CNRS, Sorbonne France University, France"],"raw_orcid":"https://orcid.org/0000-0003-0056-2831","affiliations":[{"raw_affiliation_string":"CNRS and Sorbonne University, France","institution_ids":["https://openalex.org/I39804081","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"CNRS, Sorbonne France University, France","institution_ids":["https://openalex.org/I182627622","https://openalex.org/I51101395","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103069356"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I182627622","https://openalex.org/I39804081","https://openalex.org/I51101395"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3379224,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"32","issue":"1","first_page":"999","last_page":"1009"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.33880001306533813,"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":0.33880001306533813,"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":0.13860000669956207,"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/T12772","display_name":"Control and Stability of Dynamical Systems","score":0.09049999713897705,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.6553000211715698},{"id":"https://openalex.org/keywords/isomorphism","display_name":"Isomorphism (crystallography)","score":0.5048999786376953},{"id":"https://openalex.org/keywords/electron-density","display_name":"Electron density","score":0.5037999749183655},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.4848000109195709},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.4758000075817108},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.396699994802475},{"id":"https://openalex.org/keywords/density-functional-theory","display_name":"Density functional theory","score":0.3928999900817871},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.3871000111103058},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.36000001430511475}],"concepts":[{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.6553000211715698},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5647000074386597},{"id":"https://openalex.org/C203436722","wikidata":"https://www.wikidata.org/wiki/Q902950","display_name":"Isomorphism (crystallography)","level":3,"score":0.5048999786376953},{"id":"https://openalex.org/C125485243","wikidata":"https://www.wikidata.org/wiki/Q905186","display_name":"Electron density","level":3,"score":0.5037999749183655},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.4848000109195709},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.4758000075817108},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.41339999437332153},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.396699994802475},{"id":"https://openalex.org/C152365726","wikidata":"https://www.wikidata.org/wiki/Q1048589","display_name":"Density functional theory","level":2,"score":0.3928999900817871},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.3871000111103058},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.36000001430511475},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.35589998960494995},{"id":"https://openalex.org/C147120987","wikidata":"https://www.wikidata.org/wiki/Q2225","display_name":"Electron","level":2,"score":0.35190001130104065},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3467000126838684},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.33550000190734863},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.32820001244544983},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3149999976158142},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3140000104904175},{"id":"https://openalex.org/C155673373","wikidata":"https://www.wikidata.org/wiki/Q1648886","display_name":"Structural stability","level":2,"score":0.31209999322891235},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3091000020503998},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.303600013256073},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.2996000051498413},{"id":"https://openalex.org/C63385615","wikidata":"https://www.wikidata.org/wiki/Q2869600","display_name":"Atoms in molecules","level":3,"score":0.28790000081062317},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.28290000557899475},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2728999853134155},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2669000029563904},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.26339998841285706},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.2599000036716461},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2596000134944916},{"id":"https://openalex.org/C176321772","wikidata":"https://www.wikidata.org/wiki/Q1430640","display_name":"Numerical stability","level":3,"score":0.25940001010894775},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.25519999861717224},{"id":"https://openalex.org/C124600460","wikidata":"https://www.wikidata.org/wiki/Q842809","display_name":"Bond order","level":4,"score":0.25189998745918274}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tvcg.2025.3634636","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2025.3634636","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},{"id":"pmid:41379924","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41379924","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":"IEEE transactions on visualization and computer graphics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3484067271","display_name":null,"funder_award_id":"2020/38/E/ST4/00614","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G465780485","display_name":null,"funder_award_id":"ERC-2019-COG","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":82,"referenced_works":["https://openalex.org/W81006425","https://openalex.org/W178628026","https://openalex.org/W1503771062","https://openalex.org/W1523084549","https://openalex.org/W1523441917","https://openalex.org/W1604082823","https://openalex.org/W1920826835","https://openalex.org/W1927021626","https://openalex.org/W1930589737","https://openalex.org/W1963821710","https://openalex.org/W1972862231","https://openalex.org/W1979364624","https://openalex.org/W1990982370","https://openalex.org/W2005989959","https://openalex.org/W2006329201","https://openalex.org/W2008423326","https://openalex.org/W2008581147","https://openalex.org/W2010799271","https://openalex.org/W2020185622","https://openalex.org/W2028046413","https://openalex.org/W2030976617","https://openalex.org/W2037613900","https://openalex.org/W2053227378","https://openalex.org/W2057869046","https://openalex.org/W2063831812","https://openalex.org/W2075608792","https://openalex.org/W2096510084","https://openalex.org/W2112777640","https://openalex.org/W2120568174","https://openalex.org/W2126364917","https://openalex.org/W2128934301","https://openalex.org/W2141460641","https://openalex.org/W2141461755","https://openalex.org/W2142345929","https://openalex.org/W2146019744","https://openalex.org/W2150345533","https://openalex.org/W2152167878","https://openalex.org/W2157514509","https://openalex.org/W2157701289","https://openalex.org/W2302648258","https://openalex.org/W2325955172","https://openalex.org/W2475195788","https://openalex.org/W2483548563","https://openalex.org/W2506414821","https://openalex.org/W2549327495","https://openalex.org/W2558911530","https://openalex.org/W2614596590","https://openalex.org/W2753153359","https://openalex.org/W2789480745","https://openalex.org/W2791166933","https://openalex.org/W2793477525","https://openalex.org/W2804691503","https://openalex.org/W2888965192","https://openalex.org/W2902125368","https://openalex.org/W2907543882","https://openalex.org/W2951435719","https://openalex.org/W2962844619","https://openalex.org/W2994761520","https://openalex.org/W2997113231","https://openalex.org/W3013843370","https://openalex.org/W3085701794","https://openalex.org/W3088405390","https://openalex.org/W3091564511","https://openalex.org/W3119625501","https://openalex.org/W3138447845","https://openalex.org/W3175951774","https://openalex.org/W3193608265","https://openalex.org/W4210889101","https://openalex.org/W4240050210","https://openalex.org/W4249104873","https://openalex.org/W4255383393","https://openalex.org/W4280502173","https://openalex.org/W4289688996","https://openalex.org/W4313421805","https://openalex.org/W4317496753","https://openalex.org/W4387701746","https://openalex.org/W4389043381","https://openalex.org/W4391421620","https://openalex.org/W4391735053","https://openalex.org/W4396670505","https://openalex.org/W4400065185","https://openalex.org/W4404238953"],"related_works":[],"abstract_inverted_index":{"This":[0],"application":[1],"paper":[2],"investigates":[3],"the":[4,13,55,86,109,113,123,136,153],"stability":[5,67,119],"of":[6,16,26,34,59,83,112,126,155],"hydrogen":[7],"bonds":[8],"(H-bonds),":[9],"as":[10],"characterized":[11],"by":[12,45,140],"Quantum":[14],"Theory":[15],"Atoms":[17],"in":[18],"Molecules":[19],"(QTAIM).":[20],"First,":[21],"we":[22,63],"contribute":[23],"a":[24,65,102],"database":[25,161],"4544":[27],"electron":[28,115,159],"densities":[29,127],"associated":[30],"to":[31],"four":[32],"isomers":[33],"water":[35],"hexamers":[36],"(the":[37],"so-called":[38],"Ring,":[39],"Book,":[40],"Cage":[41],"and":[42,146,162],"Prism),":[43],"generated":[44],"distorting":[46],"their":[47],"equilibrium":[48,79],"geometry":[49],"under":[50],"various":[51],"structural":[52],"perturbations,":[53],"modeling":[54],"natural":[56],"dynamic":[57],"behavior":[58],"molecular":[60],"systems.":[61],"Second,":[62],"present":[64,77],"new":[66,118],"measure,":[68],"called":[69,94],"bond":[70,75],"occurrence":[71,84],"rate,":[72],"associating":[73],"each":[74],"path":[76],"at":[78,168],"with":[80],"its":[81,97],"rate":[82],"within":[85],"input":[87],"ensemble.":[88],"We":[89],"also":[90],"provide":[91],"an":[92],"algorithm,":[93],"BondMatcher,":[95],"for":[96,122,151],"automatic":[98,124],"computation,":[99],"based":[100],"on":[101],"tailored,":[103],"geometry-aware":[104],"partial":[105],"isomorphism":[106],"estimation":[107],"between":[108],"extremum":[110],"graphs":[111],"considered":[114],"densities.":[116],"Our":[117,158],"measure":[120],"allows":[121],"identification":[125],"lacking":[128],"H-bond":[129,156],"paths,":[130],"enabling":[131],"further":[132],"visual":[133],"inspections.":[134],"Specifically,":[135],"topological":[137],"analysis":[138],"enabled":[139],"our":[141,163],"framework":[142],"corroborates":[143],"experimental":[144],"observations":[145],"provides":[147],"refined":[148],"geometrical":[149],"criteria":[150],"characterizing":[152],"disappearance":[154],"paths.":[157],"density":[160],"C++":[164],"implementation":[165],"are":[166],"available":[167],"this":[169],"address:":[170],"https://github.com/thom-dani/BondMatcher.":[171]},"counts_by_year":[],"updated_date":"2026-02-09T05:59:30.833894","created_date":"2025-11-02T00:00:00"}
