Related papers: Protein token: a dynamic unit in protein interacti…
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
In this paper, we consider the statistical analysis of a protein interaction network. We propose a Bayesian model that uses a hierarchy of probabilistic assumptions about the way proteins interact with one another in order to: (i) identify…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitful developments in protein language models (pLMs). A key…
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially…
Recently a technique based on the interaction between adhesion proteins extracted from Streptococcus pyogenes, known as SpyRing, has been widely used to improve the thermal resilience of enzymes, the assembly of biostructures, cancer cell…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…
Deep neural networks, particularly Transformers, have been widely adopted for predicting the functional properties of proteins. In this work, we focus on exploring whether Protein Transformers can capture biological intelligence among…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…
Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…