Science | ProteinMPNN : 基于深度学习的蛋白序列设计 本文介绍华盛顿大学的蛋白质设计科学家D. Baker在2022年9月15发表在Science研究工作Robust deep learning–based protein sequence design using ProteinMPNN。研究团队开发了一种基于深度学习的蛋白质序列设计方法 ProteinMPNN,它在计算机和实验测试中均具有出色的性能。
Where possible, these methods are introduced with case studies that have validated generated sequences in vitro. Figure 1 summarizes these three applications of generative models. In addition, we provide an overview of common deep generative models for protein sequences, variational autoencoders (V...
Deep learning Protein design Neural networks Protein structure Protein structure design Protein sequence design Introduction Proteins with three-dimensional (3D) structures leverage the spatial organization of amino acids to achieve function. An enzyme active site, for example, may involve a network of hy...
Protein sequence design with deep generative models Zachary Wu, Kadina E. Johnston, Frances H. Arnold, Kevin K. Yang Current Opinion in Chemical Biology 65 • note • 2021 Structure-based protein design with deep learning Ovchinnikov, Sergey, and Po-Ssu Huang Current opinion in chemical biolo...
Protein sequence design by deep learningThe design of protein sequences that can precisely fold into pre-specified 3D structures is a challenging task. A recently proposed deep-learning algorithm improves such designs when compared with traditional, physics-based protein design approaches....
The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein...
第二条路就是RFDesign/TrDesign的思路,通过间接建模P(Sequence | Structure):根据贝叶斯公式: P(Sequence | Structure) * P(Structure) = P(Structure | Sequence)* P(Sequence),可得P(Sequence | Structure) = P(Structure | Sequence)* P(Sequence)/P(Structure),P(Structure | Sequence)是结构预测模型所...
Deep learning has emerged as a promising approach for tackling this problem by ... Protein sequence design on given backbones with deep learning Yufeng Liu and Haiyan Liu Protein Engineering, Design and Selection, Volume 37, 2024, gzad024, https://doi.org/10.1093/protein/gzad024 Deep ...
Solving a mystery that stumped scientists for decades, last November a group of computational biologists from Alphabet’s DeepMind used AI to predict a protein’s structure from its amino acid sequence. Not even a year later, a new study offers a more powerful model, capable of computing protei...
deep-learning protein-sequences representation-learning language-model sequence-embedding protein-embedding Updated Jun 16, 2021 Python J-SNACKKB / FLIP Star 96 Code Issues Pull requests A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of prote...