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The unsparse coexpression data exhibits low node degree bias (the mean AUC based on node degree ranking is 0.52) but very good performance using the prediction algorithm (mean AUC of 0.71, Figure 6A).
Potential Atx3 NES signals were identified by consensus to the ΦX1 3ΦX2 3ΦXΦ motif (Φ indicates a large hydrophobic residue, and X indicates any amino acid), and using the prediction algorithm NetNES (http://www.cbs.dtu.dk/databases/NESbase-1.0 [43]), and fused to Rev(1.4 -GFP fusion protein (the plasmid encoding Rev(1.4 -GFP was kindly provided by Beric R. Henderson).
Second, we used a candidate-based approach using the prediction algorithm RNA22 to screen all the genes implicated in DDR for miRNA recognition element of miR-1255b, miR-148b*, and miR-193b*.
Helical content of peptides were calculated using the prediction algorithm developed by Serrano's group (AGADIR) with an amide group at the C-terminal and an acetyl group at the N-terminal region.
Our results demonstrated that fusion peptides composed of a highly-immunogenic epitope and a poorly-immunoreactive tumor-associated antigen can effectively activate host immunity, and furthermore, using the prediction algorithm SYFPEITHI to enhance the affinity of antigen presentation, the resulting fusion peptides provoked even stronger immune responses.
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We searched for putative targets of each family using the prediction algorithms of PicTar, TargetScan, and MiRBase.
Further, using the prediction-correction algorithm, the lower-order symmetric mechanisms are utilized to lead the structure smoothly transform into expected bifurcation paths.
Also, the parameters in (19) and (20) are estimated using the prediction error minimization (PEM) algorithm here, with the objective of minimizing prediction errors.
Tertiary structures of Smprx6 were predicted using the SWISSMODEL prediction algorithm (http://swissmodel.expasy.org).org
We predicted sRNA targets using the Comparative Prediction Algorithm for sRNA Targets (CopraRNA) server [ 17].
The target of our study, the Ndel1 protein was predicted to be unstructured using the FoldIndex prediction algorithm (http://bip.weizmann.ac.il/fldbin/findex) (Prilusky et al., 2005), with the exception of approximately fifty amino acids surrounding amino acid 250 (Fig. 1A).
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