相关论文: Protein structure prediction by an iterative searc…

Recent advances in geometric deep learning and generative modeling have enabled the design of novel proteins with a wide range of desired properties. However, current state-of-the-art approaches are typically restricted to generating…

Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…

A novel Genetic Algorithm is described that is suitable for determining the global minimum energy configurations of crystal structures and which can also be used as a polymorph search technique. This algorithm requires no prior assumptions…

In nonadaptive group testing, the main research objective is to design an efficient algorithm to identify a set of up to $t$ positive elements among $n$ samples with as few tests as possible. Disjunct matrices and separable matrices are two…

A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…

The simultaneous orthogonal matching pursuit (SOMP) algorithm aims to find the joint support of a set of sparse signals acquired under a multiple measurement vector model. Critically, the analysis of SOMP depends on the maximal inner…

In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…

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…

One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long timescales. To overcome this bottleneck, we…

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring…

The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

We demonstrate a machine learning approach designed to extract hidden chemistry/physics to facilitate new materials discovery. In particular, we propose a novel method for learning latent knowledge from material structure data in which…

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is…

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a…

Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…

This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…

Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…

Poor diet and nutrition in the United States has immense financial and health costs, and development of new tools for diet planning could help families better balance their financial and temporal constraints with the quality of their diet…

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…