ColabFold: making protein folding accessible to all
TL;DR: ColabFold as discussed by the authors combines the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold for protein folding and achieves 40-60fold faster search and optimized model utilization.
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Abstract: ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40-60-fold faster search and optimized model utilization enables prediction of close to 1,000 structures per day on a server with one graphics processing unit. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at https://github.com/sokrypton/ColabFold and its novel environmental databases are available at https://colabfold.mmseqs.com .
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OUP accepted manuscript
10 Feb 2022
TL;DR: In this article , the authors identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineralization.
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Next-generation ABACUS biosensors reveal cellular ABA dynamics driving root growth at low aerial humidity
James B. Rowe,Mathieu J Grangé-Guermente,Marino Exposito-Rodriguez,Rinukshi Wimalasekera,Martin Lenz,Kartika N. Shetty,Sean R. Cutler,Alexander M. Jones +7 more
TL;DR: In this paper , the authors developed ABACUS2s-next-generation Förster resonance energy transfer (FRET) biosensors for ABA with high affinity, signal-to-noise ratio and orthogonality.
A blast fungus zinc-finger fold effector binds to a hydrophobic pocket in host Exo70 proteins to modulate immune recognition in rice
Juan Carlos De la Concepcion,Koki Fujisaki,A Bentham,Neftaly Cruz Mireles,Victor Sanchez de Medina Hernandez,Motoki Shimizu,David M. Lawson,Sophien Kamoun,Ryohei Terauchi,Mark J. Banfield +9 more
TL;DR: The data suggest that blast fungus ZiF effectors bind a conserved Exo70 interface to manipulate plant exocytosis and that these effectors are also baited by plant immune receptors, pointing to new opportunities for engineering disease resistance.
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PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes
Dario F. Marzella,F. M. Parizi,Derek van Tilborg,Nicolas Renaud,Daan Sybrandi,Rafaella Buzatu,Daniel Rademaker,Peter A C 't Hoen,Li C. Xue +8 more
TL;DR: PANDORA is a modularized and user-configurable python package with easy installation that performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed.
Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers.
Kazumori Mise,Yoko Masuda,Keishi Senoo,Hideomi Itoh +3 more
- 17 Nov 2021
TL;DR: In this article, the authors exhaustively analyzed genomes in RefSeq (231,908 genomes) and KEGG (6,509 genomes), and found hundreds of pseudo-nifH-harboring genomes.
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