Abstract AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind
that can predict three-dimensional (3D) structures of proteins from amino acid sequences …

Learning effective protein representations is critical in a variety of tasks in biology such as
predicting protein function or structure. Existing approaches usually pretrain protein …

This paper demonstrates that language models are strong structure-based protein
designers. We present LM-Design, a generic approach to reprogramming sequence-based …

Large-scale protein language models (PLMs), such as the ESM family, have achieved
remarkable performance in various downstream tasks related to protein structure and …

In recent years, generative protein sequence models have been developed to sample novel
sequences. However, predicting whether generated proteins will fold and function remains …

In the field of protein engineering, the function and structure of proteins are key to
understanding cellular mechanisms, biological evolution, and biodiversity. With the …

Homologous protein search is one of the most commonly used methods for protein
annotation and analysis. Compared to structure search, detecting distant evolutionary …

This paper introduces diffusion protein language model (DPLM), a versatile protein
language model that demonstrates strong generative and predictive capabilities for protein …

We are now witnessing significant progress of deep learning methods in a variety of tasks
(or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the …

Large Language Models (LLMs) have revolutionized the field of natural language
processing, but they fall short in comprehending biological sequences such as proteins. To …