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Repo for CLAPE framework

This repo holds the code of CLAPE (Contrastive Learning And Pre-trained Encoder) framework for protein-ligands binding sites prediction. We provide 3 ligand-binding tasks including protein-DNA, protein-RNA, and antibody-antigen binding sites prediction.

CLAPE is primarily dependent on a large-scale pre-trained protein language model ProtBert implemented using HuggingFace's Transformers and PyTorch. Please install the dependencies in advance.

Usage:

We provide the Python script for predicting ligand-binding sites of given protein sequences in FASTA format. Here we provide a sample file, and please use CLAPE as following commands:

python clape.py --input example.fa --output out.txt

This command will first load the pre-trained models, users can specify the downloading directory using the --cache parameter.

Some parameters are described as follows:

Parameters Descriptions
--help Show the help doc.
--ligand Specify the ligand for prediction, DNA, RNA, and AB (antibody) are supported now, default: DNA.
--threshold Specify the threshold for identifying the binding site, the value needs to be between 0 and 1, default: 0.5.
--input The path of the input file in FASTA format.
--output The path of the output file, the first and the second line are the same as the input file, and the third line is the prediction result.
--cache The path for saving the pre-trained parameters, default: protbert.

Reference:

Protein-DNA binding sites prediction based on pre-trained protein language model and contrastive learning by Yufan Liu and Boxue Tian. Published in Briefings in Bioinformatics.

Please contact [email protected] for questions.

clape's People

Contributors

yandrewl avatar

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