相关论文: Optimization and evaluation of a coarse-grained mo…

Interactions between proteins are hard to decipher. Protein-protein interactions are difficult problem to address because they are not based on differences in charge type like protein-DNA or protein-lipid interactions. In this manuscript we…

Protein dynamics play a crucial role in many biological processes and drug interactions. However, measuring, and simulating protein dynamics is challenging and time-consuming. While machine learning holds promise in deciphering the…

Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a…

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…

Gaussian network model (GNM) is one of the most accurate and efficient methods for biomolecular flexibility analysis. However, the systematic generalization of the GNM has been elusive. We show that the GNM Kirchhoff matrix can be built…

In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to…

In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological…

High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…

Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…

In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated…

Genetic interactions confer robustness on cells in response to genetic perturbations. This often occurs through molecular buffering mechanisms that can be predicted using, among other features, the degree of coexpression between genes,…

Coherent nonlinear optical micro-spectroscopy is a frequently used tool in modern material science, as it is sensitive to many different local observables, which comprise, among others, crystal symmetry and vibrational properties. The…

We introduce an RG-inspired coarse-graining for extracting the collective features of data. The key to successful coarse-graining lies in finding appropriate pairs of data sets. We coarse-grain the two closest data in a regular real-space…

Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer protein chains…

Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…

Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…

We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…

The generation of protein crystals is necessary for the study of protein molecular function and structure. This is done empirically by processing large numbers of crystallization trials and inspecting them regularly in search of those with…

In many stochastic simulations of biochemical reaction networks, it is desirable to ``coarse-grain'' the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed,…