Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification
Publication Date
October 05, 2017
Journal
PLOS ONE
Authors
Jakub Jończyk, Barbara Malawska & Marek Bajda
Volume
12
Issue
10
Pages
e0186108
DOI
https://dx.plos.org/10.1371/journal.pone.0186108
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0186108
Scopus
85030722772
Mendeley
http://www.mendeley.com/research/hybrid-approach-structure-modeling-histamine-h3-receptor-multilevel-assessment-tool-model-verificati-1
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Mendeley | Further Information

{"title"=>"Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification", "type"=>"journal", "authors"=>[{"first_name"=>"Jakub", "last_name"=>"Jończyk", "scopus_author_id"=>"35976133000"}, {"first_name"=>"Barbara", "last_name"=>"Malawska", "scopus_author_id"=>"55913729000"}, {"first_name"=>"Marek", "last_name"=>"Bajda", "scopus_author_id"=>"15847912200"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-85030722772", "sgr"=>"85030722772", "pui"=>"618616377", "isbn"=>"1111111111", "pmid"=>"28982153", "doi"=>"10.1371/journal.pone.0186108"}, "id"=>"9fde7d36-41d5-341a-a840-bc6848a791be", "abstract"=>"The crucial role of G-protein coupled receptors and the significant achievements associated with a better understanding of the spatial structure of known receptors in this family encouraged us to undertake a study on the histamine H3 receptor, whose crystal structure is still unresolved. The latest literature data and availability of different software enabled us to build homology models of higher accuracy than previously published ones. The new models are expected to be closer to crystal structures; and therefore, they are much more helpful in the design of potential ligands. In this article, we describe the generation of homology models with the use of diverse tools and a hybrid assessment. Our study incorporates a hybrid assessment connecting knowledge-based scoring algorithms with a two-step ligand-based docking procedure. Knowledge-based scoring employs probability theory for global energy minimum determination based on information about native amino acid conformation from a dataset of experimentally determined protein structures. For a two-step docking procedure two programs were applied: GOLD was used in the first step and Glide in the second. Hybrid approaches offer advantages by combining various theoretical methods in one modeling algorithm. The biggest advantage of hybrid methods is their intrinsic ability to self-update and self-refine when additional structural data are acquired. Moreover, the diversity of computational methods and structural data used in hybrid approaches for structure prediction limit inaccuracies resulting from theoretical approximations or fuzziness of experimental data. The results of docking to the new H3 receptor model allowed us to analyze ligand-receptor interactions for reference compounds.", "link"=>"http://www.mendeley.com/research/hybrid-approach-structure-modeling-histamine-h3-receptor-multilevel-assessment-tool-model-verificati-1", "reader_count"=>4, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Researcher"=>1, "Student > Ph. D. Student"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Researcher"=>1, "Student > Ph. D. Student"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>1}, "reader_count_by_subdiscipline"=>{"Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>3}}, "group_count"=>1}

Scopus | Further Information

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