Related papers: Amino Acid Interaction Network Prediction using Mu…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
Complex systems often involve higher-order interactions which require us to go beyond their description in terms of pairwise networks. Triadic interactions are a fundamental type of higher-order interaction that occurs when one node…
In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…
Interaction between users in online social networks plays a key role in social network analysis. One on important types of social group is full connected relation between some users, which known as clique structure. Therefore finding a…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
A multilayer network depicts different types of interactions among the same set of nodes. For example, protease networks consist of five to seven layers, where different layers represent distinct types of experimentally confirmed molecule…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
Link prediction algorithms can help to understand the structure and dynamics of complex systems, to reconstruct networks from incomplete data sets and to forecast future interactions in evolving networks. Available algorithms based on…
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…
Protein representation learning is a challenging task that aims to capture the structure and function of proteins from their amino acid sequences. Previous methods largely ignored the fact that not all amino acids are equally important for…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…
An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative…
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
The Saccharomyces cerevisiae protein-protein interaction map, as well as many natural and man-made networks, shares the scale-free topology. The preferential attachment model was suggested as a generic network evolution model that yields…
Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine.…