Related papers: Rapid simulation of protein motion: merging flexib…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
Fluid-structure simulations of slender inextensible filaments in a viscous fluid are often plagued by numerical stiffness. Recent coarse-graining studies have reduced the computational requirements of simulating such systems, though have…
Proteins are made of atoms constantly fluctuating, but can occasionally undergo large-scale changes. Such transitions are of biological interest, linking the structure of a protein to its function with a cell. Atomic-level simulations, such…
Rigidity analysis using the "pebble game" can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
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…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
A fast computer algorithm, the pebble game, has been used successfully to study rigidity percolation on 2D elastic networks, as well as on a special class of 3D networks, the bond-bending networks. Application of the pebble game approach to…
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…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…