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Foldy: An open-source web application for interactive protein structure analysis.
Roberts, Jacob B; Nava, Alberto A; Pearson, Allison N; Incha, Matthew R; Valencia, Luis E; Ma, Melody; Rao, Abhay; Keasling, Jay D.
Afiliación
  • Roberts JB; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.
  • Nava AA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
  • Pearson AN; Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America.
  • Incha MR; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.
  • Valencia LE; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
  • Ma M; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America.
  • Rao A; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.
  • Keasling JD; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
PLoS Comput Biol ; 20(2): e1011171, 2024 Feb.
Article en En | MEDLINE | ID: mdl-38306398
ABSTRACT
Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy's interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy's interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Proteínas Límite: Humans Idioma: En Revista: PLoS Comput Biol Asunto de la revista: BIOLOGIA / INFORMATICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Proteínas Límite: Humans Idioma: En Revista: PLoS Comput Biol Asunto de la revista: BIOLOGIA / INFORMATICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos