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Hi, I have a problem with it. In my vcf file ,there are snps in those proteins. But, the message remains no snps, what is point? Thank you! No SNPs in >=1000 contiguous codons. If this was unexpected,…
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Dear Elo Lab,
I am very interested in your RolDE approach and would like to apply it to my project. However, when I tried to work on your sample data, I found out that without setting a seed, the res…
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Hello everyone. I am doing some evaluation jobs of the inference pipeline. I am wondering how to evaluate the result pdb file such like TM-score, for those proteins that CASP14 doesn't provide the r…
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Hi,
Thank you for your tool. We would like to ask where the data for protein DmkA was obtained from. We didn't find the protein sequence of DmkA in NR database. And the proteins annotated as DmkA u…
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```
import os
import pandas as pd
import csv
import oddt
from oddt.scoring.functions import RFScore
oddt.toolkit = oddt.toolkits.rdk
rf = rfscore(version=1, n_jobs=-1)
# rf.load('/path/to/…
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Can you provide more details about your training, such as the source of the training data? Is it necessary for the crosslink data to represent a 25A distance between two proteins in a complex? Also, c…
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The following screenshot is of the speciality proteins for a genome. It is not obvious what version of CARD this was generated from. I think that it should be listed either in the table or side bar.
…
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Hi,
I was wondering if the SHOOT website has an API or some way to submit proteins via command line? I have a few hundreds genes I'd like to run through SHOOT to identify orthologs.
Thanks
Jon
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For a process (WikiPathways pathway, GO term, or pathway ontology term) find all proteins involved and see how many are expressed in a specific tissue or cell type (using NextPot as the source for exp…
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Dear author,
Thanks for your excellent work. I have some VLP enrichment samples from the animal gut. When I use the tool, how to select the parameter "--enrichment_preset". The default is "human",…