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Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and pepti...

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Detalles Bibliográficos
Autores principales: Rao, H. B., Zhu, F., Yang, G. B., Li, Z. R., Chen, Y. Z.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125735/
https://www.ncbi.nlm.nih.gov/pubmed/21609959
http://dx.doi.org/10.1093/nar/gkr284
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author Rao, H. B.
Zhu, F.
Yang, G. B.
Li, Z. R.
Chen, Y. Z.
author_facet Rao, H. B.
Zhu, F.
Yang, G. B.
Li, Z. R.
Chen, Y. Z.
author_sort Rao, H. B.
collection PubMed
description Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence. To facilitate more extensive studies of protein and peptides, numerous improvements and updates have been made to PROFEAT. We added new functions for computing descriptors of protein–protein and protein–small molecule interactions, segment descriptors for local properties of protein sequences, topological descriptors for peptide sequences and small molecule structures. We also added new feature groups for proteins and peptides (pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, total amino acid properties and atomic-level topological descriptors) as well as for small molecules (atomic-level topological descriptors). Overall, PROFEAT computes 11 feature groups of descriptors for proteins and peptides, and a feature group of more than 400 descriptors for small molecules plus the derived features for protein–protein and protein–small molecule interactions. Our computational algorithms have been extensively tested and used in a number of published works for predicting proteins of specific structural or functional classes, protein–protein interactions, peptides of specific functions and quantitative structure activity relationships of small molecules. PROFEAT is accessible free of charge at http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi.
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spelling pubmed-31257352011-07-05 Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence Rao, H. B. Zhu, F. Yang, G. B. Li, Z. R. Chen, Y. Z. Nucleic Acids Res Articles Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence. To facilitate more extensive studies of protein and peptides, numerous improvements and updates have been made to PROFEAT. We added new functions for computing descriptors of protein–protein and protein–small molecule interactions, segment descriptors for local properties of protein sequences, topological descriptors for peptide sequences and small molecule structures. We also added new feature groups for proteins and peptides (pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, total amino acid properties and atomic-level topological descriptors) as well as for small molecules (atomic-level topological descriptors). Overall, PROFEAT computes 11 feature groups of descriptors for proteins and peptides, and a feature group of more than 400 descriptors for small molecules plus the derived features for protein–protein and protein–small molecule interactions. Our computational algorithms have been extensively tested and used in a number of published works for predicting proteins of specific structural or functional classes, protein–protein interactions, peptides of specific functions and quantitative structure activity relationships of small molecules. PROFEAT is accessible free of charge at http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi. Oxford University Press 2011-07-01 2011-05-23 /pmc/articles/PMC3125735/ /pubmed/21609959 http://dx.doi.org/10.1093/nar/gkr284 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Rao, H. B.
Zhu, F.
Yang, G. B.
Li, Z. R.
Chen, Y. Z.
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
title Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
title_full Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
title_fullStr Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
title_full_unstemmed Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
title_short Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
title_sort update of profeat: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125735/
https://www.ncbi.nlm.nih.gov/pubmed/21609959
http://dx.doi.org/10.1093/nar/gkr284
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