The files required to run this page are:
1. your pdb,
2. your RNA encoder embedding, and
3. your RNA-MSM embedding
Below shows how to obtain the 2 embedding files.
Embedding 1: RNA encoder embeddings
The webserver is
http://idrblab.cn/rnaincoder/coding. After entering the website, upload your own fasta sequence file, and then select the feature to be calculated, except for all the rest of the One-hot encoding, and finally obtain a npz file containing the embedding.
Embedding 2: RNA-MSM embeddings
Firstly, you should download this repository and create the RNA-MSM environment (details can be found
here):
git clone git@github.com:yikunpku/RNA-MSM.git
cd ./RNA-MSM
conda env create -f environment.yml
conda activate RNA-MSM
Secondly, utilizing RNAcmap3 tool to search for homologous sequences of the target RNA sequences to serve as input for the RNA-MSM model. The RNAcmap3 can be found
here. After installation, run the following command:
run_rnacmap3.sh -i your.fasta -d mfdca
Thirdly, Run the RNA-MSM script to get the final embedding
python RNA_MSM_Inference.py \
data.root_path=./ \
data.MSA_path=./results \
data.model_path=./pretrained \
data.MSA_list=rna_id.txt