Related papers: Unified perspective on proteins: A physics approac…
Physicists study a wide variety of phenomena creating new interdisciplinary research fields by applying theories and methods originally developed in physics in order to solve problems in economics, social science, biology, medicine,…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
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…
Nonlinear models and optimization methods have successfully tackled a rapidly growing set of problems in recent years. Indeed, a relatively small toolbox of such models and methods can provide sufficient performance across a large landscape…
One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins…
Physics is a model of nature able to both describe and predict the results of measurements made with respect to reference systems. These reference systems, in turn, are themselves physical and thus subject to the laws of physics. The…
This is the first of a series of papers that we intend to publish about the epistemology of fundamental physics in its current state. One of the main objectives of these papers is to improve our understanding of fundamental physics (and…
This book is devoted to an informal discussion of patterns constructed for treating physical problems. Such patterns, when sufficiently formalized, are usually referred as "models", and tents to be applied not only in physics, but conquer…
Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
Two proteins are homologous if they have a common evolutionary origin, and the binary classification problem is to identify proteins in a candidate set that are homologous to a particular native protein. The feature (explanatory) variables…
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…
We study the protein folding problem on the base of the quantum approach we proposed recently by considering the model of protein chain with nine amino-acid residues. We introduced the concept of distance space and its projections on a…
From classical mechanics to quantum field theory, the physical facts at one point in space are held to be independent of those at other points in space. I propose that we can usefully challenge this orthodoxy in order to explain otherwise…
Complex systems are characterized by specific time-dependent interactions among their many constituents. As a consequence they often manifest rich, non-trivial and unexpected behavior. Examples arise both in the physical and non-physical…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…