Related papers: Methods for protein complex prediction and their c…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot…
Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…
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…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Protein-protein interaction (PPI) networks consist of the physical and/or functional interactions between the proteins of an organism. Since the biophysical and high-throughput methods used to form PPI networks are expensive,…
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the functional significance of intrinsically disordered…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a…
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…
As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across…
Background: Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom…
Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…
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 interaction (PPI) represents a central challenge within the biology field, and accurately predicting the consequences of mutations in this context is crucial for drug design and protein engineering. Deep learning (DL) has…