IMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURES
Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinformatics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these metho...
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| Format: | Article |
| Language: | English |
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Gdańsk University of Technology
2014-10-01
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| Series: | TASK Quarterly |
| Subjects: | |
| Online Access: | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/1902 |
| _version_ | 1818264453783748608 |
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| author | MARTA STRUMILLO ALEKSANDRA E. DAWID AGATA SZCZASIUK DOMINIK GRONT |
| author_facet | MARTA STRUMILLO ALEKSANDRA E. DAWID AGATA SZCZASIUK DOMINIK GRONT |
| author_sort | MARTA STRUMILLO |
| collection | DOAJ |
| description |
Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinformatics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-based modeling, which combines computational tools recently developed in our laboratory: the database of protein domain structures (BDDB) with one dimensional and three dimensional threading applications. The protocol was tested during a CASP11 experiment.
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| first_indexed | 2024-12-12T19:35:09Z |
| format | Article |
| id | doaj.art-7ff5c8d875a3412c84f926308a3fb67e |
| institution | Directory Open Access Journal |
| issn | 1428-6394 |
| language | English |
| last_indexed | 2024-12-12T19:35:09Z |
| publishDate | 2014-10-01 |
| publisher | Gdańsk University of Technology |
| record_format | Article |
| series | TASK Quarterly |
| spelling | doaj.art-7ff5c8d875a3412c84f926308a3fb67e2022-12-22T00:14:20ZengGdańsk University of TechnologyTASK Quarterly1428-63942014-10-0118410.17466/TQ2014/18.4/SIMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURESMARTA STRUMILLO0ALEKSANDRA E. DAWID1AGATA SZCZASIUK2DOMINIK GRONT3University of Warsaw, Faculty of Chemistry, Laboratory of Theory of BiopolymersUniversity of Warsaw, Faculty of Chemistry, Laboratory of Theory of BiopolymersUniversity of Warsaw, Faculty of Chemistry, Laboratory of Theory of BiopolymersUniversity of Warsaw, Faculty of Chemistry, Laboratory of Theory of Biopolymers Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinformatics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-based modeling, which combines computational tools recently developed in our laboratory: the database of protein domain structures (BDDB) with one dimensional and three dimensional threading applications. The protocol was tested during a CASP11 experiment. https://journal.mostwiedzy.pl/TASKQuarterly/article/view/1902protein structure predictioncomparative modelingprotein threadingprotein alignmentBioShellRosetta |
| spellingShingle | MARTA STRUMILLO ALEKSANDRA E. DAWID AGATA SZCZASIUK DOMINIK GRONT IMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURES TASK Quarterly protein structure prediction comparative modeling protein threading protein alignment BioShell Rosetta |
| title | IMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURES |
| title_full | IMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURES |
| title_fullStr | IMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURES |
| title_full_unstemmed | IMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURES |
| title_short | IMPLEMENTATION AND EVALUATION OF NEW PROTOCOL FOR COMPARATIVE MODELING OF PROTEIN STRUCTURES |
| title_sort | implementation and evaluation of new protocol for comparative modeling of protein structures |
| topic | protein structure prediction comparative modeling protein threading protein alignment BioShell Rosetta |
| url | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/1902 |
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