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CaviDB: a database of cavities and their features in the structural and conformational space of proteins
Proteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10171230/ https://www.ncbi.nlm.nih.gov/pubmed/37162753 http://dx.doi.org/10.1093/database/baad010 |
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author | Velez Rueda, Ana Julia Bulgarelli, Franco Leonardo Palopoli, Nicolás Parisi, Gustavo |
author_facet | Velez Rueda, Ana Julia Bulgarelli, Franco Leonardo Palopoli, Nicolás Parisi, Gustavo |
author_sort | Velez Rueda, Ana Julia |
collection | PubMed |
description | Proteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential for a mechanistic understanding of protein function. Here, we present CaviDB, a novel database of cavities and their features in known protein structures. It integrates the results of commonly used cavity detection software with protein features derived from sequence, structural and functional analyses. Each protein in CaviDB is linked to its corresponding conformers, which also facilitates the study of conformational changes in cavities. Our initial release includes ∼927 773 distinct proteins, as well as the characterization of 36 136 869 cavities, of which 1 147 034 were predicted to be drug targets. The structural focus of CaviDB provides the ability to compare cavities and their properties from different conformational states of the protein. CaviDB not only aims to provide a comprehensive database that can be used for various aspects of drug design and discovery but also contributes to a better understanding of the fundamentals of protein structure–function relationships. With its unique approach, CaviDB represents an indispensable resource for the large community of bioinformaticians in particular and biologists in general. Database URL https://www.cavidb.org |
format | Online Article Text |
id | pubmed-10171230 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-101712302023-05-11 CaviDB: a database of cavities and their features in the structural and conformational space of proteins Velez Rueda, Ana Julia Bulgarelli, Franco Leonardo Palopoli, Nicolás Parisi, Gustavo Database (Oxford) Original Article Proteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential for a mechanistic understanding of protein function. Here, we present CaviDB, a novel database of cavities and their features in known protein structures. It integrates the results of commonly used cavity detection software with protein features derived from sequence, structural and functional analyses. Each protein in CaviDB is linked to its corresponding conformers, which also facilitates the study of conformational changes in cavities. Our initial release includes ∼927 773 distinct proteins, as well as the characterization of 36 136 869 cavities, of which 1 147 034 were predicted to be drug targets. The structural focus of CaviDB provides the ability to compare cavities and their properties from different conformational states of the protein. CaviDB not only aims to provide a comprehensive database that can be used for various aspects of drug design and discovery but also contributes to a better understanding of the fundamentals of protein structure–function relationships. With its unique approach, CaviDB represents an indispensable resource for the large community of bioinformaticians in particular and biologists in general. Database URL https://www.cavidb.org Oxford University Press 2023-05-10 /pmc/articles/PMC10171230/ /pubmed/37162753 http://dx.doi.org/10.1093/database/baad010 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (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 | Original Article Velez Rueda, Ana Julia Bulgarelli, Franco Leonardo Palopoli, Nicolás Parisi, Gustavo CaviDB: a database of cavities and their features in the structural and conformational space of proteins |
title | CaviDB: a database of cavities and their features in the structural and conformational space of proteins |
title_full | CaviDB: a database of cavities and their features in the structural and conformational space of proteins |
title_fullStr | CaviDB: a database of cavities and their features in the structural and conformational space of proteins |
title_full_unstemmed | CaviDB: a database of cavities and their features in the structural and conformational space of proteins |
title_short | CaviDB: a database of cavities and their features in the structural and conformational space of proteins |
title_sort | cavidb: a database of cavities and their features in the structural and conformational space of proteins |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10171230/ https://www.ncbi.nlm.nih.gov/pubmed/37162753 http://dx.doi.org/10.1093/database/baad010 |
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