AN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATION
CASP (Critical Assessment of protein Structure Prediction) is a community-wide experiment for protein structure prediction taking place every two years since 1994. In CASP11 held in 2014, according to the official CASP11 assessment, our method named `nns' was ranked as the second best server m...
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| Format: | Article |
| Language: | English |
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Gdańsk University of Technology
2016-10-01
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| Series: | TASK Quarterly |
| Subjects: | |
| Online Access: | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/1824 |
| _version_ | 1817984384395902976 |
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| author | KEEHYOUNG JOO INSUK JOUNG JOOYOUNG LEE |
| author_facet | KEEHYOUNG JOO INSUK JOUNG JOOYOUNG LEE |
| author_sort | KEEHYOUNG JOO |
| collection | DOAJ |
| description |
CASP (Critical Assessment of protein Structure Prediction) is a community-wide experiment for protein structure prediction taking place every two years since 1994. In CASP11 held in 2014, according to the official CASP11 assessment, our method named `nns' was ranked as the second best server method based on models ranked as first out of 81 targets. In `nns', we applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For the fold recognition, a new alignment method called CRFalign was used. The good performance of the nns server method is attributed to the successful fold recognition carried out by combined methods including CRFalign, and the current modeling formulation incorporating accurate structural aspects collected from multiple templates. In this article, we provide a successful example of `nns' predictions for T0776, for which all details of intermediate modeling data are provided.
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| first_indexed | 2024-04-13T23:43:59Z |
| format | Article |
| id | doaj.art-ef5f8fe15a75443d974c6b2d2862f241 |
| institution | Directory Open Access Journal |
| issn | 1428-6394 |
| language | English |
| last_indexed | 2024-04-13T23:43:59Z |
| publishDate | 2016-10-01 |
| publisher | Gdańsk University of Technology |
| record_format | Article |
| series | TASK Quarterly |
| spelling | doaj.art-ef5f8fe15a75443d974c6b2d2862f2412022-12-22T02:24:24ZengGdańsk University of TechnologyTASK Quarterly1428-63942016-10-0120410.17466/tq2016/20.4/bAN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATIONKEEHYOUNG JOO0INSUK JOUNG1JOOYOUNG LEE2Center for In Silico Protein Science, Center for Advanced ComputationKorea Institute for Advanced Study, Center for In Silico Protein Science, School of Computational SciencesKorea Institute for Advanced Study, Center for In Silico Protein Science, Center for Advanced Computation, School of Computational Sciences CASP (Critical Assessment of protein Structure Prediction) is a community-wide experiment for protein structure prediction taking place every two years since 1994. In CASP11 held in 2014, according to the official CASP11 assessment, our method named `nns' was ranked as the second best server method based on models ranked as first out of 81 targets. In `nns', we applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For the fold recognition, a new alignment method called CRFalign was used. The good performance of the nns server method is attributed to the successful fold recognition carried out by combined methods including CRFalign, and the current modeling formulation incorporating accurate structural aspects collected from multiple templates. In this article, we provide a successful example of `nns' predictions for T0776, for which all details of intermediate modeling data are provided. https://journal.mostwiedzy.pl/TASKQuarterly/article/view/1824template based modelingprotein structure modelingglobal optimizationcasphomology modelingsequence alignment |
| spellingShingle | KEEHYOUNG JOO INSUK JOUNG JOOYOUNG LEE AN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATION TASK Quarterly template based modeling protein structure modeling global optimization casp homology modeling sequence alignment |
| title | AN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATION |
| title_full | AN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATION |
| title_fullStr | AN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATION |
| title_full_unstemmed | AN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATION |
| title_short | AN EXAMPLE OF TEMPLATE BASED PROTEIN STRUCTURE MODELING BY GLOBAL OPTIMIZATION |
| title_sort | example of template based protein structure modeling by global optimization |
| topic | template based modeling protein structure modeling global optimization casp homology modeling sequence alignment |
| url | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/1824 |
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