2026-09-25T22:39:59Z https://epublications.vu.lt/oai

oai:vu.lt:elaba:31079741 2026-07-07T18:39:39Z openaireNDLTDDRIVERDART-EUROPE

Extraction and usage of crystallographic knowledge for refinement and validation of molecular models /Kristalografinės informacijos išgavimas bei panaudojimas molekulių modelių tikslinimui ir tikrinimui.Merkys, Andrius,info:eu-repo/semantics/openAccessCrystallography Open Database ; validation ; geometryThis 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.Institutional Repository of Vilnius UniversityGražulis, Sauliusinfo:eu-repo/semantics/doctoralThesiseng2018application/pdfhttps://epublications.vu.lt/object/elaba:31079741/31079741.pdfhttps://repository.vu.lt/VU:ELABAETD31079741&prefLang=en_US