AIMC Topic: Proteins
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Medium-sized protein language models perform well at transfer learning on realistic datasets.
Scientific reports
Jul 1, 2025
Protein language models (pLMs) can offer deep insights into evolutionary and structural properties of proteins. While larger models, such as the 15 billion parameter model ESM-2, promise to capture more complex patterns in sequence space, they also p...
SE(3)-equivariant ternary complex prediction towards target protein degradation.
Nature communications
Jul 1, 2025
Targeted protein degradation (TPD) has rapidly emerged as a powerful modality for drugging previously "undruggable" proteins. TPD employs small molecules like PROTACs and molecular glue degraders (MGD) to induce target protein degradation via the for...
'Intelligent' proteins.
Cellular and molecular life sciences : CMLS
Jun 14, 2025
We present an idea of protein molecules that challenges the traditional view of proteins as simple molecular machines and suggests instead that they exhibit a basic form of "intelligence". The idea stems from suggestions coming from Integrated Inform...
High-Throughput Analysis of Protein Adsorption to a Large Library of Polymers Using Liquid Extraction Surface Analysis-Tandem Mass Spectrometry (LESA-MS/MS).
Analytical chemistry
Jun 10, 2025
Biomaterials play an important role in medicine from contact lenses to joint replacements. High-throughput screening coupled with machine learning has identified synthetic polymers that prevent bacterial biofilm formation, prevent fungal cell attachm...
Designing diverse and high-performance proteins with a large language model in the loop.
PLoS computational biology
Jun 5, 2025
We present a protein engineering approach to directed evolution with machine learning that integrates a new semi-supervised neural network fitness prediction model, Seq2Fitness, and an innovative optimization algorithm, biphasic annealing for diverse...
Measuring alignment of structural proteins in engineered tissue constructs using polarized Raman spectroscopy.
PloS one
May 30, 2025
Measures of structural protein alignment within biological and engineered tissues are needed for improved understanding of their mechanical behavior and functionality. We advance our method of measuring protein alignment using polarized Raman spectro...
Prediction of drug-target interactions based on substructure subsequences and cross-public attention mechanism.
PloS one
May 30, 2025
Drug-target interactions (DTIs) play a critical role in drug discovery and repurposing. Deep learning-based methods for predicting drug-target interactions are more efficient than wet-lab experiments. The extraction of original and substructural feat...
Explainability of Protein Deep Learning Models.
International journal of molecular sciences
May 29, 2025
Protein embeddings are the new main source of information about proteins, producing state-of-the-art solutions to many problems, including protein interaction prediction, a fundamental issue in proteomics. Understanding the embeddings and what causes...
Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.
eLife
May 27, 2025
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
EMOCPD: Efficient Attention-Based Models for Computational Protein Design Using Amino Acid Microenvironment.
Journal of chemical information and modeling
May 26, 2025
Computational protein design (CPD) refers to the use of computational methods to design proteins. Traditional methods relying on energy functions and heuristic algorithms for sequence design are inefficient and do not meet the demands of the big data...
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