Foldy: An open-source web application for interactive protein structure analysis.

Autor: Roberts JB; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.; Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America., Nava AA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America., Pearson AN; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.; Department of Plant and Microbial Biology, 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.; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America., Valencia LE; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America., Ma M; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America., Rao A; Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America., Keasling JD; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.; Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America.; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America.; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, People's Republic of China.; The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Denmark.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2024 Feb 02; Vol. 20 (2), pp. e1011171. Date of Electronic Publication: 2024 Feb 02 (Print Publication: 2024).
DOI: 10.1371/journal.pcbi.1011171
Abstrakt: 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.
Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: J.D.K. has relationships with and financial interests in Lygos, Demetrix, Apertor Labs, Ansa Biosciences, Cyklos Materials, Elsevier, Center for Biosustainability at Technical University of Denmark, Shenzhen Institute of Advanced Technology, Napigen, Kalion, Praj, Zero Acre Farms, ResVita Bio, Orbillion, and Keasling Consulting. J.B.R. has financial interests in AlkaLi Labs.
(Copyright: © 2024 Roberts et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje