[HTML][HTML] Protein representations: Encoding biological information for machine learning in biocatalysis

D Harding-Larsen, J Funk, NG Madsen… - Biotechnology …, 2024 - Elsevier
Enzymes offer a more environmentally friendly and low-impact solution to conventional
chemistry, but they often require additional engineering for their application in industrial …

Simple, efficient, and scalable structure-aware adapter boosts protein language models

Y Tan, M Li, B Zhou, B Zhong, L Zheng… - Journal of Chemical …, 2024 - ACS Publications
Fine-tuning pretrained protein language models (PLMs) has emerged as a prominent
strategy for enhancing downstream prediction tasks, often outperforming traditional …

How the technologies behind self‐driving cars, social networks, ChatGPT, and DALL‐E2 are changing structural biology

M Bochtler - BioEssays, 2024 - Wiley Online Library
The performance of deep Neural Networks (NNs) in the text (ChatGPT) and image (DALL‐
E2) domains has attracted worldwide attention. Convolutional NNs (CNNs), Large …

Structure-informed protein language models are robust predictors for variant effects

Y Sun, Y Shen - Human Genetics, 2024 - Springer
Emerging variant effect predictors, protein language models (pLMs) learn evolutionary
distribution of functional sequences to capture fitness landscape. Considering that variant …

MetalPrognosis: A Biological Language Model-Based Approach for Disease-Associated Mutations in Metal-Binding Site Prediction

R Jia, Z He, C Wang, X Guo, F Li - IEEE/ACM Transactions on …, 2024 - ieeexplore.ieee.org
Protein-metal ion interactions play a central role in the onset of numerous diseases. When
amino acid changes lead to missense mutations in metal-binding sites, the disrupted …

ProtEx: A Retrieval-Augmented Approach for Protein Function Prediction

P Shaw, B Gurram, D Belanger, A Gane, ML Bileschi… - bioRxiv, 2024 - biorxiv.org
Mapping a protein sequence to its underlying biological function is a critical problem of
increasing importance in biology. In this work, we propose ProtEx, a retrieval-augmented …

Into the Void: Cavities and Tunnels are Essential for Functional Protein Design

J Zhang, Z Peng - bioRxiv, 2024 - biorxiv.org
The design of functional proteins is crucial as it enables the creation of tailored proteins with
specific capabilities, unlocking the potential solutions to various biomedical and industrial …

MMSite: A Multi-modal Framework for the Identification of Active Sites in Proteins

S Ouyang, H Cai, Y Luo, K Su, L Zhang, B Du - The Thirty-eighth Annual … - openreview.net
The accurate identification of active sites in proteins is essential for the advancement of life
sciences and pharmaceutical development, as these sites are of critical importance for …