Related papers: Leveraging Multi-modal Representations to Predict …

Machine learning has revolutionized polymer science by enabling rapid property prediction and generative design. Large language models (LLMs) offer further opportunities in polymer informatics by simplifying workflows that traditionally…

Protein language models (pLMs) produce per-residue representations that capture evolutionary and structural information, yet their mean-pooled sequence embeddings are not explicitly trained to reflect functional, evolutionary or structural…

We introduce TemPL, a novel deep learning approach for zero-shot prediction of protein stability and activity, harnessing temperature-guided language modeling. By assembling an extensive dataset of 96 million sequence-host bacterial strain…

Molecular dynamics (MD) is a central computational tool in physics, chemistry, and biology, enabling quantitative prediction of experimental observables as expectations over high-dimensional molecular distributions such as Boltzmann…

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…

Multimodal protein features play a crucial role in protein function prediction. However, these features encompass a wide range of information, ranging from structural data and sequence features to protein attributes and interaction…

While protein language models (PLMs) are one of the most promising avenues of research for future de novo protein design, the way in which they transform sequences to hidden representations, as well as the information encoded in such…

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…

Protein language models (PLMs) have emerged as powerful tools to detect complex patterns of protein sequences. However, the capability of PLMs to fully capture information on protein sequences might be limited by focusing on single…

Language Models (LMs) excel in understanding textual descriptions of proteins, as evident in biomedical question-answering tasks. However, their capability falters with raw protein data, such as amino acid sequences, due to a deficit in…

Accurate prediction of enzymatic activity from amino acid sequences could drastically accelerate enzyme engineering for applications such as bioremediation and therapeutics development. In recent years, Protein Language Model (PLM)…

In this study, we expand upon the FLIP benchmark-designed for evaluating protein fitness prediction models in small, specialized prediction tasks-by assessing the performance of state-of-the-art large protein language models, including…

AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step…

Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological…

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the…

Multi-sample aggregation strategies, such as majority voting and best-of-N sampling, are widely used in contemporary large language models (LLMs) to enhance predictive accuracy across various tasks. A key challenge in this process is…

Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…

Motivation: Site directed mutagenesis is widely used to understand the structure and function of biomolecules. Computational prediction of protein mutation impacts offers a fast, economical and potentially accurate alternative to laboratory…

Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other properties. The emergence of deep learning methods for…

Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…