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The FunFOLD2 server for the prediction of protein–ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our functio...

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Detalles Bibliográficos
Autores principales: Roche, Daniel B., Buenavista, Maria T., McGuffin, Liam J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692132/
https://www.ncbi.nlm.nih.gov/pubmed/23761453
http://dx.doi.org/10.1093/nar/gkt498
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author Roche, Daniel B.
Buenavista, Maria T.
McGuffin, Liam J.
author_facet Roche, Daniel B.
Buenavista, Maria T.
McGuffin, Liam J.
author_sort Roche, Daniel B.
collection PubMed
description The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.
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spelling pubmed-36921322013-06-25 The FunFOLD2 server for the prediction of protein–ligand interactions Roche, Daniel B. Buenavista, Maria T. McGuffin, Liam J. Nucleic Acids Res Articles The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html. Oxford University Press 2013-07 2013-06-11 /pmc/articles/PMC3692132/ /pubmed/23761453 http://dx.doi.org/10.1093/nar/gkt498 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Roche, Daniel B.
Buenavista, Maria T.
McGuffin, Liam J.
The FunFOLD2 server for the prediction of protein–ligand interactions
title The FunFOLD2 server for the prediction of protein–ligand interactions
title_full The FunFOLD2 server for the prediction of protein–ligand interactions
title_fullStr The FunFOLD2 server for the prediction of protein–ligand interactions
title_full_unstemmed The FunFOLD2 server for the prediction of protein–ligand interactions
title_short The FunFOLD2 server for the prediction of protein–ligand interactions
title_sort funfold2 server for the prediction of protein–ligand interactions
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692132/
https://www.ncbi.nlm.nih.gov/pubmed/23761453
http://dx.doi.org/10.1093/nar/gkt498
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