相关论文: Quantitative Molecular Scaling Theory of Protein A…
Scaling describes how a given quantity $Y$ that characterizes a system varies with its size $P$. For most complex systems it is of the form $Y\sim P^\beta$ with a nontrivial value of the exponent $\beta$, usually determined by regression…
A scaling theory is developed for diffusion-limited cluster aggregation in a porous medium, where the primary particles and clusters stick irreversibly to the walls of the pore space as well as to each other. Three scaling regimes are…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Mass scaling is widely used in finite element models of structural dynamics for increasing the critical time step of explicit time integration methods. While the field has been flourishing over the years, it still lacks a strong theoretical…
Protein folding -- the problem of predicting the spatial structure of a protein given its sequence of amino-acids -- has attracted considerable research effort in biochemistry in recent decades. In this work, we explore the potential of…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
Tokenization is a promising path to multi-modal models capable of jointly understanding protein sequences, structure, and function. Existing protein structure tokenizers create tokens by pooling information from local neighborhoods, an…
As a function of connectivity, spring networks exhibit a critical transition between floppy and rigid phases at an isostatic threshold. For connectivity below this threshold, fiber networks were recently shown theoretically to exhibit a…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
Most physical and other natural systems are complex entities composed of a large number of interacting individual elements. It is a surprising fact that they often obey the so-called scaling laws relating an observable quantity with a…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…
Scale invariance is a central organizing principle in physics, underlying phenomena that range from critical behaviour in statistical mechanics to transport and chaos in nonlinear dynamical systems. Here we present a unified and physically…
Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
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…