Machine learning for evolutionary-based and physicsinspired protein design: Current and future synergies Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson, Jérôme Tubiana Current Opinion in Structural Biology De novo design of polyhedral protein assemblies: before and after the AI revoluti...
These experiments were repeated three times with similar results using independent biological samples. Extended Data Fig. 7 Characterization of aY-modified iNap1 (NADPH sensor). a, Fluorescence excitation (dash line) and emission (solid line) profiles for iNap1 before (cyan) and after (dark cyan...
5a–c). Importantly, LoRNA provides cell-wide quantification of RNA localization before and after stimulation. This allowed us to uncover that, upon activation of the UPR, although many cytosolic mRNAs migrate to granules, membrane mRNAs do so at a higher proportion (Fig. 5d). However, not ...
gradient_accumulation_steps: int, number of updates steps to accumulate before performing a backward/update pass, default: 1. learning_rate: float, the initial learning rate for Adam, default: 1e-4. num_train_epochs: int, the total number of training epochs to perform, default: 50. logging...
48h after seeding HEK293T cells were transfected using lipofectamine reagent METAFECTENE™ (Biontex, Germany). For each cell culture dish 36 μl METAFECTENE™ and 36 μg total DNA was used whereby 5 ml MEM was removed before transfection. The transfection procedure was done according to ...
1A). Both before and after TEV cleavage, GFP fluorescence was evenly distributed, indicating that neither C1 nor C2 formed biomolecular condensates under these conditions, corroborating recent results (41). Of note, the lack of LLPS was not due to inefficient TEV cleavage (Fig. 1C, right ...
In our study, HLECSs were stimulated with BMP-4 for 2 h before and after oxida- tive stress, and the expression of caspase-3 decreased signifi- cantly. However, when we measured the expression of caspase-3 in cells that were only pretreated with BMP-4 under oxidative stress, there was ...
The original models could not predict a free energy landscape consistent with the experimental results (Supplementary Figs. 9 and 10), because they assumed that the continuous region (C, D, and E helices) must fold before the discontinuous region (consisting of A and B helices on the N-...
aFSC curves of PSII tetramer reconstruction before (dark) and after (green) removing false positives by sorting method. The final resolution reached 3.9 Å after adding more micrographs (red).bReconstruction of PSII tetramer at 3.9 Å.c3D reconstruction resolved by GisSPA with aM. pneu...
To show that this principle is universally applicable, beyond the cell line and cancer tissue cases that we investigated before (16), we used it to estimate the concentrations of different diagnostically relevant proteins or protein classes in blood plasma after digesting plasma proteins using the ...