{"id":{"repo_id":"vilnius","oai_identifier":"oai:vu.lt:elaba:31079741"},"canonical_url":"https://search.dev.ndltd.org/etd/vilnius/oai:vu.lt:elaba:31079741","repository":{"repo_id":"vilnius","name":"Vilnius University","base_url":"https://epublications.vu.lt/oai"},"display":{"title":"Extraction and usage of crystallographic knowledge for refinement and validation of molecular models /","abstract":"This dissertation describes fully automated means to extract geometric information – interatomic bond lengths, bond and dihedral angles – from small-molecule crystal structures, and to use this information for the validation of novel crystal structures. Crystallography Open Database (COD), regularly updated open-access resource of small-molecule crystal structures, has been chosen as the source of input data. Software has been developed to prefilter the records from the COD, transform them to a form appropriate for geometric analysis, extract and organise the geometric parameters. Statistical models chosen to describe the groups of chemically similar observations can be used for Bayesian method-based outlier detection: previously unseen, or seen relatively rarely, geometric observations in molecules in consideration are spotted and marked for further analysis. Software implementing this principle has been developed and a Web based user interface has been presented. The method for structure validation has been tested with novel, retracted and deliberately deformed small-molecule crystal structures. The main conclusions of this dissertation are that the COD is a proper resource for small-molecule geometric information, developed methods and software tools are sufficient to organise the data from the source database into a library of molecular geometry, which is in turn capable to spot unusual geometric features in small-molecule crystal structures.","abstract_html":"This dissertation describes fully automated means to extract geometric information – interatomic bond lengths, bond and dihedral angles – from small-molecule crystal structures, and to use this information for the validation of novel crystal structures. Crystallography Open Database (COD), regularly updated open-access resource of small-molecule crystal structures, has been chosen as the source of input data. Software has been developed to prefilter the records from the COD, transform them to a form appropriate for geometric analysis, extract and organise the geometric parameters. Statistical models chosen to describe the groups of chemically similar observations can be used for Bayesian method-based outlier detection: previously unseen, or seen relatively rarely, geometric observations in molecules in consideration are spotted and marked for further analysis. Software implementing this principle has been developed and a Web based user interface has been presented. The method for structure validation has been tested with novel, retracted and deliberately deformed small-molecule crystal structures. The main conclusions of this dissertation are that the COD is a proper resource for small-molecule geometric information, developed methods and software tools are sufficient to organise the data from the source database into a library of molecular geometry, which is in turn capable to spot unusual geometric features in small-molecule crystal structures.","abstract_has_math":false,"creators":["Merkys, Andrius,"],"institution":"Institutional Repository of Vilnius University","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Gražulis, Saulius"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2018,"date_issued":"2018","date_published":"2018","updated_at":"2026-07-24T05:55:31Z","subjects":["Crystallography Open Database ; validation ; geometry"],"languages":["eng"],"rights":["info:eu-repo/semantics/openAccess"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://repository.vu.lt/VU:ELABAETD31079741&prefLang=en_US","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Gražulis, Saulius"]},{"key":"dc:creator","label":"Author","values":["Merkys, Andrius,"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2018"]},{"key":"dc:publisher","label":"Institution","values":["Institutional Repository of Vilnius University"]},{"key":"dc:relation","label":"Dc Relation","values":["https://epublications.vu.lt/object/elaba:31079741/31079741.pdf"]},{"key":"dc:type","label":"Dc Type","values":["info:eu-repo/semantics/doctoralThesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Crystallography Open Database ; validation ; geometry"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["info:eu-repo/semantics/openAccess"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://repository.vu.lt/VU:ELABAETD31079741&prefLang=en_US"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["This dissertation describes fully automated means to extract geometric information – interatomic bond lengths, bond and dihedral angles – from small-molecule crystal structures, and to use this information for the validation of novel crystal structures. Crystallography Open Database (COD), regularly updated open-access resource of small-molecule crystal structures, has been chosen as the source of input data. Software has been developed to prefilter the records from the COD, transform them to a form appropriate for geometric analysis, extract and organise the geometric parameters. Statistical models chosen to describe the groups of chemically similar observations can be used for Bayesian method-based outlier detection: previously unseen, or seen relatively rarely, geometric observations in molecules in consideration are spotted and marked for further analysis. Software implementing this principle has been developed and a Web based user interface has been presented. The method for structure validation has been tested with novel, retracted and deliberately deformed small-molecule crystal structures. The main conclusions of this dissertation are that the COD is a proper resource for small-molecule geometric information, developed methods and software tools are sufficient to organise the data from the source database into a library of molecular geometry, which is in turn capable to spot unusual geometric features in small-molecule crystal structures."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Extraction and usage of crystallographic knowledge for refinement and validation of molecular models /","Kristalografinės informacijos išgavimas bei panaudojimas molekulių modelių tikslinimui ir tikrinimui."]}]}],"canonical_facts":{"dc:contributor":["Gražulis, Saulius"],"dc:creator":["Merkys, Andrius,"],"dc:date":["2018"],"dc:description":["This dissertation describes fully automated means to extract geometric information – interatomic bond lengths, bond and dihedral angles – from small-molecule crystal structures, and to use this information for the validation of novel crystal structures. Crystallography Open Database (COD), regularly updated open-access resource of small-molecule crystal structures, has been chosen as the source of input data. Software has been developed to prefilter the records from the COD, transform them to a form appropriate for geometric analysis, extract and organise the geometric parameters. Statistical models chosen to describe the groups of chemically similar observations can be used for Bayesian method-based outlier detection: previously unseen, or seen relatively rarely, geometric observations in molecules in consideration are spotted and marked for further analysis. Software implementing this principle has been developed and a Web based user interface has been presented. The method for structure validation has been tested with novel, retracted and deliberately deformed small-molecule crystal structures. The main conclusions of this dissertation are that the COD is a proper resource for small-molecule geometric information, developed methods and software tools are sufficient to organise the data from the source database into a library of molecular geometry, which is in turn capable to spot unusual geometric features in small-molecule crystal structures."],"dc:format":["application/pdf"],"dc:identifier":["https://repository.vu.lt/VU:ELABAETD31079741&prefLang=en_US"],"dc:language":["eng"],"dc:publisher":["Institutional Repository of Vilnius University"],"dc:relation":["https://epublications.vu.lt/object/elaba:31079741/31079741.pdf"],"dc:rights":["info:eu-repo/semantics/openAccess"],"dc:subject":["Crystallography Open Database ; validation ; geometry"],"dc:title":["Extraction and usage of crystallographic knowledge for refinement and validation of molecular models /","Kristalografinės informacijos išgavimas bei panaudojimas molekulių modelių tikslinimui ir tikrinimui."],"dc:type":["info:eu-repo/semantics/doctoralThesis"]},"updated_at":"2026-07-24T05:55:31Z"}