相关论文: The role of evolutionary selection in the dynamics…

Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…

Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…

We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…

We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…

Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer…

The analysis of coevolution of residues in homologous proteins is a powerful tool to predict their native conformation. The standard framework in which coevolutionary analysis is usually worked out is that of equilibrium Potts models,…

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…

Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…

Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…

Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…

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…

A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…

Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found…

We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…

The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…

The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…

Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…