Related papers: Fast and Anisotropic Flexibility-Rigidity Index

The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to…

Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional…

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…

Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on…

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…

Ultrasound-based elasticity imaging is a non-invasive technique for estimating tissue stiffness fields from displacement fields obtained by comparing ultrasound signals before and after compression. While recent deep learning approaches…

The microstructure analyses of porous media have considerable research value for the study of macroscopic properties. As the premise of conducting these analyses, the accurate reconstruction of microstructure digital model is also an…

We recently proposed a method called Material Fingerprinting for the rapid discovery of mechanical material models that avoids solving continuous optimization problems. Material Fingerprinting assumes that each material exhibits a unique…

In this paper, we consider the problem of estimating finite rate of innovation (FRI) signals from noisy measurements, and specifically analyze the interaction between FRI techniques and the underlying sampling methods. We first obtain a…

We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…

Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…

Machine learning and the use of neural networks has increased precipitously over the past few years primarily due to the ever-increasing accessibility to data and the growth of computation power. It has become increasingly easy to harness…

The remarkable success of AlphaFold2 in providing accurate atomic-level prediction of protein structures from their amino acid sequence has transformed approaches to the protein folding problem. However, its core paradigm of mapping one…

Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…

Both numerical simulations and observational evidence indicate that the outer regions of galaxies and dark matter haloes are typically mildly to significantly radially anisotropic. The inner regions can be significantly non-isotropic,…

Fragment-based assembly has been widely used in Ab initio protein folding simulation which can effectively reduce the conformational space and thus accelerate sampling. The efficiency of fragment-based movement as well as the quality of…

Completely random measures (CRMs) and their normalizations (NCRMs) offer flexible models in Bayesian nonparametrics. But their infinite dimensionality presents challenges for inference. Two popular finite approximations are truncated finite…

Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…