Related papers: Effective Protein-Protein Interaction Exploration …
We propose a novel approach for predicting protein-peptide interactions using a bi-modal transformer architecture that learns an inter-facial joint distribution of residual contacts. The current data sets for crystallized protein-peptide…
The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
Protein-protein interactions are of great importance in biochemical processes. Accurate prediction of protein-protein interaction sites (PPIs) is crucial for our understanding of biological mechanism. Although numerous approaches have been…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
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…
Protein-protein interaction (PPI) prediction plays a pivotal role in deciphering cellular functions and disease mechanisms. To address the limitations of traditional experimental methods and existing computational approaches in cross-modal…
Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language…
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a…
Drug discovery (DD) has tremendously contributed to maintaining and improving public health. Hypothesizing that inhibiting protein misfolding can slow disease progression, researchers focus on target identification (Target ID) to find…
Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally…
Protein interactions constitute the fundamental building block of almost every life activity. Identifying protein communities from Protein-Protein Interaction (PPI) networks is essential to understand the principles of cellular organization…
The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…
Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps…
In this paper, a new method for PPI (proteinprotein interaction) prediction is proposed. In PPI prediction, a reliable and sufficient number of training samples is not available, but a large number of unlabeled samples is in hand. In the…
Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement…
PPI network alignment aims to find topological and functional similarities between networks of different species. Several alignment approaches have been proposed. Each of these approaches relies on a different alignment method and uses…
Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we relate conservation, essentiality and functional repertoire of a gene to the connectivity $k$ (i.e., the number of interaction…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
Over the last few years, several computational techniques have been devised to recover protein complexes from the protein interaction (PPI) networks of organisms. These techniques model "dense" subnetworks within PPI networks as complexes.…