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DISTEVAL: a web server for evaluating predicted protein distances
BACKGROUND: Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binned’ distograms, which are a more finely grained variant of the binary contact pr...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788990/ https://www.ncbi.nlm.nih.gov/pubmed/33407077 http://dx.doi.org/10.1186/s12859-020-03938-z |
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author | Adhikari, Badri Shrestha, Bikash Bernardini, Matthew Hou, Jie Lea, Jamie |
author_facet | Adhikari, Badri Shrestha, Bikash Bernardini, Matthew Hou, Jie Lea, Jamie |
author_sort | Adhikari, Badri |
collection | PubMed |
description | BACKGROUND: Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binned’ distograms, which are a more finely grained variant of the binary contact prediction problem. The latter has been introduced as a new challenge in the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14) 2020 experiment. Despite the recent proliferation of methods for predicting distances, few methods exist for evaluating these predictions. Currently only numerical metrics, which evaluate the entire prediction at once, are used. These give no insight into the structural details of a prediction. For this reason, new methods and tools are needed. RESULTS: We have developed a web server for evaluating predicted inter-residue distances. Our server, DISTEVAL, accepts predicted contacts, distances, and a true structure as optional inputs to generate informative heatmaps, chord diagrams, and 3D models. All of these outputs facilitate visual and qualitative assessment. The server also evaluates predictions using other metrics such as mean absolute error, root mean squared error, and contact precision. CONCLUSIONS: The visualizations generated by DISTEVAL complement each other and collectively serve as a powerful tool for both quantitative and qualitative assessments of predicted contacts and distances, even in the absence of a true 3D structure. |
format | Online Article Text |
id | pubmed-7788990 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-77889902021-01-07 DISTEVAL: a web server for evaluating predicted protein distances Adhikari, Badri Shrestha, Bikash Bernardini, Matthew Hou, Jie Lea, Jamie BMC Bioinformatics Software BACKGROUND: Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binned’ distograms, which are a more finely grained variant of the binary contact prediction problem. The latter has been introduced as a new challenge in the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14) 2020 experiment. Despite the recent proliferation of methods for predicting distances, few methods exist for evaluating these predictions. Currently only numerical metrics, which evaluate the entire prediction at once, are used. These give no insight into the structural details of a prediction. For this reason, new methods and tools are needed. RESULTS: We have developed a web server for evaluating predicted inter-residue distances. Our server, DISTEVAL, accepts predicted contacts, distances, and a true structure as optional inputs to generate informative heatmaps, chord diagrams, and 3D models. All of these outputs facilitate visual and qualitative assessment. The server also evaluates predictions using other metrics such as mean absolute error, root mean squared error, and contact precision. CONCLUSIONS: The visualizations generated by DISTEVAL complement each other and collectively serve as a powerful tool for both quantitative and qualitative assessments of predicted contacts and distances, even in the absence of a true 3D structure. BioMed Central 2021-01-06 /pmc/articles/PMC7788990/ /pubmed/33407077 http://dx.doi.org/10.1186/s12859-020-03938-z Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Adhikari, Badri Shrestha, Bikash Bernardini, Matthew Hou, Jie Lea, Jamie DISTEVAL: a web server for evaluating predicted protein distances |
title | DISTEVAL: a web server for evaluating predicted protein distances |
title_full | DISTEVAL: a web server for evaluating predicted protein distances |
title_fullStr | DISTEVAL: a web server for evaluating predicted protein distances |
title_full_unstemmed | DISTEVAL: a web server for evaluating predicted protein distances |
title_short | DISTEVAL: a web server for evaluating predicted protein distances |
title_sort | disteval: a web server for evaluating predicted protein distances |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788990/ https://www.ncbi.nlm.nih.gov/pubmed/33407077 http://dx.doi.org/10.1186/s12859-020-03938-z |
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