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DeepRefiner: high-accuracy protein structure refinement by deep network calibration
The DeepRefiner webserver, freely available at http://watson.cse.eng.auburn.edu/DeepRefiner/, is an interactive and fully configurable online system for high-accuracy protein structure refinement. Fuelled by deep learning, DeepRefiner offers the ability to leverage cutting-edge deep neural network a...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262753/ https://www.ncbi.nlm.nih.gov/pubmed/33999209 http://dx.doi.org/10.1093/nar/gkab361 |
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author | Shuvo, Md Hossain Gulfam, Muhammad Bhattacharya, Debswapna |
author_facet | Shuvo, Md Hossain Gulfam, Muhammad Bhattacharya, Debswapna |
author_sort | Shuvo, Md Hossain |
collection | PubMed |
description | The DeepRefiner webserver, freely available at http://watson.cse.eng.auburn.edu/DeepRefiner/, is an interactive and fully configurable online system for high-accuracy protein structure refinement. Fuelled by deep learning, DeepRefiner offers the ability to leverage cutting-edge deep neural network architectures which can be calibrated for on-demand selection of adventurous or conservative refinement modes targeted at degree or consistency of refinement. The method has been extensively tested in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments under the group name ‘Bhattacharya-Server’ and was officially ranked as the No. 2 refinement server in CASP13 (second only to ‘Seok-server’ and outperforming all other refinement servers) and No. 2 refinement server in CASP14 (second only to ‘FEIG-S’ and outperforming all other refinement servers including ‘Seok-server’). The DeepRefiner web interface offers a number of convenient features, including (i) fully customizable refinement job submission and validation; (ii) automated job status update, tracking, and notifications; (ii) interactive and interpretable web-based results retrieval with quantitative and visual analysis and (iv) extensive help information on job submission and results interpretation via web-based tutorial and help tooltips. |
format | Online Article Text |
id | pubmed-8262753 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-82627532021-07-08 DeepRefiner: high-accuracy protein structure refinement by deep network calibration Shuvo, Md Hossain Gulfam, Muhammad Bhattacharya, Debswapna Nucleic Acids Res Web Server Issue The DeepRefiner webserver, freely available at http://watson.cse.eng.auburn.edu/DeepRefiner/, is an interactive and fully configurable online system for high-accuracy protein structure refinement. Fuelled by deep learning, DeepRefiner offers the ability to leverage cutting-edge deep neural network architectures which can be calibrated for on-demand selection of adventurous or conservative refinement modes targeted at degree or consistency of refinement. The method has been extensively tested in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments under the group name ‘Bhattacharya-Server’ and was officially ranked as the No. 2 refinement server in CASP13 (second only to ‘Seok-server’ and outperforming all other refinement servers) and No. 2 refinement server in CASP14 (second only to ‘FEIG-S’ and outperforming all other refinement servers including ‘Seok-server’). The DeepRefiner web interface offers a number of convenient features, including (i) fully customizable refinement job submission and validation; (ii) automated job status update, tracking, and notifications; (ii) interactive and interpretable web-based results retrieval with quantitative and visual analysis and (iv) extensive help information on job submission and results interpretation via web-based tutorial and help tooltips. Oxford University Press 2021-05-17 /pmc/articles/PMC8262753/ /pubmed/33999209 http://dx.doi.org/10.1093/nar/gkab361 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Shuvo, Md Hossain Gulfam, Muhammad Bhattacharya, Debswapna DeepRefiner: high-accuracy protein structure refinement by deep network calibration |
title | DeepRefiner: high-accuracy protein structure refinement by deep network calibration |
title_full | DeepRefiner: high-accuracy protein structure refinement by deep network calibration |
title_fullStr | DeepRefiner: high-accuracy protein structure refinement by deep network calibration |
title_full_unstemmed | DeepRefiner: high-accuracy protein structure refinement by deep network calibration |
title_short | DeepRefiner: high-accuracy protein structure refinement by deep network calibration |
title_sort | deeprefiner: high-accuracy protein structure refinement by deep network calibration |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262753/ https://www.ncbi.nlm.nih.gov/pubmed/33999209 http://dx.doi.org/10.1093/nar/gkab361 |
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