[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 …
chemistry, but they often require additional engineering for their application in industrial …
Simple, efficient, and scalable structure-aware adapter boosts protein language models
Fine-tuning pretrained protein language models (PLMs) has emerged as a prominent
strategy for enhancing downstream prediction tasks, often outperforming traditional …
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 …
E2) domains has attracted worldwide attention. Convolutional NNs (CNNs), Large …
Structure-informed protein language models are robust predictors for variant effects
Emerging variant effect predictors, protein language models (pLMs) learn evolutionary
distribution of functional sequences to capture fitness landscape. Considering that variant …
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
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 …
amino acid changes lead to missense mutations in metal-binding sites, the disrupted …
ProtEx: A Retrieval-Augmented Approach for Protein Function Prediction
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 …
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 …
specific capabilities, unlocking the potential solutions to various biomedical and industrial …
MMSite: A Multi-modal Framework for the Identification of Active Sites in Proteins
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 …
sciences and pharmaceutical development, as these sites are of critical importance for …