Related papers: Redundancies in Large-scale Protein Interaction Ne…
Algorithms that detect covariance between pairs of columns in multiple sequence alignments are commonly employed to predict functionally important residues and structural contacts. However, the assumption that co-variance only occurs…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
We test the claim by Yu et al. -- presented in Science 322, 104 (2008) -- that the degree distribution of the yeast (Saccharomyces cerevisiae) protein-interaction network is best approximated by a power law. Yu et al. consider three…
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…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
Our results demonstrated that a previously reported protein name co-occurrence method (5-mention PubGene) which was not based on a hypothesis testing framework, it is generally statistically more significant than the 99th percentile of…
Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.…
We present a simple model for the underlying structure of protein-protein pairwise interaction graphs that is based on the way in which proteins attach to each other in experiments such as yeast two-hybrid assays. We show that data on the…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…