ESM蛋白质语言模型学习笔记一

abbyabley

已于 2024-04-23 12:25:01 修改

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于 2024-04-23 11:49:41 首次发布

本文链接：https://blog.csdn.net/weixin_43950953/article/details/137270033

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安装

可以参考官方文档：facebookresearch/esm: Evolutionary Scale Modeling (esm): Pretrained language models for proteins (github.com)

在服务器上，安装使用

pip install fair-esm

esm2的使用，官方示例

import torch
import esm

# Load ESM-2 model
model, alphabet = esm.pretrained.esm2_t33_650M_UR50D()
batch_converter = alphabet.get_batch_converter()
model.eval()  # disables dropout for deterministic results

# Prepare data (first 2 sequences from ESMStructuralSplitDataset superfamily / 4)
data = [
    ("protein1", "MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGG"),
    ("protein2", "KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEE"),
    ("