Related papers: The network of stabilizing contacts in proteins st…

It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…

Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…

Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…

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…

Interdependence is a fundamental ingredient to analyze the stability of many real-world complex systems featuring functional liasons. Yet, physical realizations of this coupling are still unknown, due to the lack of a theoretical framework…

The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…

Reconstructing the structural connectivity between interacting units from observed activity is a challenge across many different disciplines. The fundamental first step is to establish whether or to what extent the interactions between the…

Reconstruction of structure and parameters of an Ising model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine…

What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…

Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo…

Inverse problems in statistical physics are motivated by the challenges of `big data' in different fields, in particular high-throughput experiments in biology. In inverse problems, the usual procedure of statistical physics needs to be…

The idea of this project is to study the protein structure and sequence relationship using the hidden markov model and artificial neural network. In this context we have assumed two hidden markov models. In first model we have taken protein…

Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-consuming molecular dynamics (MD) simulations conducted in silico. Recent advances in generative…

Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…

Gene expression data, or transcription data, are surrogates for actual protein concentrations in the cells. In addition protein-protein interactions are static diagrams of all the protein-protein interactions in the cell. These interactions…

We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…

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…

Temporal networks of face-to-face interactions between individuals are useful proxies of the dynamics of social systems on fast time scales. Several empirical statistical properties of these networks have been shown to be robust across a…