In this communication, we introduce a new structure-based affinity predictor for protein-protein complexes. This predictor, dubbed PCANN (Protein Complex Affinity by Neural Network), uses the ESM-2 language model to encode the information about prote...
Tools available for inferring enzyme function from general sequence, fold, or evolutionary information are generally successful. However, they can lead to misclassification if a deviation in local structural features influences the function. Here, we...
Understanding protein structures can facilitate the development of therapeutic drugs. Traditionally, protein structures have been determined through experimental approaches such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy...
Protein structure prediction has undergone significant advancements, driven by the limitations of experimental techniques like X-ray crystallography, NMR, and cryo-EM, which are costly and time-consuming. To bridge the gap between protein sequences a...
Journal of chemical theory and computation
Mar 13, 2025
Protein evolution has shaped enzymes that maintain stability and function across diverse thermal environments. While sequence variation, thermal stability and conformational dynamics are known to influence an enzyme's thermal adaptation, how these fa...
Current opinion in structural biology
Mar 12, 2025
Recent years have seen tremendous developments in the use of machine learning models to link amino-acid sequence, structure, and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and sequences th...
Protein allostery is a fundamental biological regulatory mechanism that allows communication between distant locations within a protein, modifying its function in response to signals. Experimental techniques, such as NMR spectroscopy and cryo-electro...
Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches developed to address this prob...
Current opinion in structural biology
Feb 21, 2025
Large Language Models for proteins, namely protein Language Models (pLMs), have begun to provide an important alternative to capturing the information encoded in a protein sequence in computers. Arguably, pLMs have advanced importantly to understandi...
Journal of chemical information and modeling
Feb 21, 2025
Proteins are inherently dynamic, and their conformational ensembles play a crucial role in biological function. Large-scale motions may govern the protein structure-function relationship, and numerous transient but stable conformations of intrinsical...
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