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Hello,
I am curious about the strand1 and strand2 columns in arriba output. I read in the documentation that the strand before "/" is the strand of the gene from the gtf and the second strand (that…
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The API produces amino acid level output such as:
"hgvs_predicted_protein_consequence": {
"slr": "NP_000080.2:p.(G1018D)",
"tlr": "NP_000080.2(LRG_2p1):p.(Gly1018Asp)"
}
T…
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Table 3 and Table S5 In the [bioRxiv manuscript for DConStruct](https://doi.org/10.1101/2020.07.05.188466) show that DConStruct outperforms the best state-of-the-art method, DMPfold, on 40 CASP FM tar…
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Hi there,
Robert and I have written an OpenMM command line executable which is planned to be in the next release. It can be downloaded here:
https://github.com/rmcgibbo/openmm-cmd.git
I've also ma…
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Hi,
I'm a post-doc from Fudan university, China. I have just read your paper "SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction", wh…
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I am attempting to reproduce the results in your paper and then train models on my own dataset, but several models failed to train, saying "ValueError: cannot reshape array"
Any idea on how to fix …
ghost updated
3 years ago
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Hey there,
I am currently on a project using the large molecule model setting in my simulations. However the default settings do not describe my data very well.
cmax is generally overestimated, wh…
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Concerns asa, ta, ssec, sseb, disorder, disorderb, disorderc.
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Hi!
Wonderful work here, and wonderful code aswell.
I have a few questions regarding your model and some of your input preparation steps.
1- Why do you implemented padding as a new class and not a…
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Disclaimer: I'm not a structural biologist and I'm not working in protein structure prediction. I can't say I've understood all the details here.
I've read the the AlphaFold publication and was so …