相关论文: Comparative analysis of protein structure using mu…

Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…

Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…

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…

In this paper, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root-mean-square deviation (RMSD) characterization and employs a series expansion of the protein's shape function in terms…

Learning from 3D protein structures has gained wide interest in protein modeling and structural bioinformatics. Unfortunately, the number of available structures is orders of magnitude lower than the training data sizes commonly used in…

Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…

Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…

On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact…

Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…

The protein backbone is described as a smooth curved and twisted line in three-dimensional (3D) space and characterized by its curvature $\kappa(s)$ and torsion $\tau(s)$ both expressed as a function of arc length s. It is shown that the…

The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…

Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…

Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…

Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…

Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…

The structural analysis of shape boundaries leads to the characterization of objects as well as to the understanding of shape properties. The literature on graphs and networks have contributed to the structural characterization of shapes…

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of…

We present a robust method to find region-level correspondences between shapes, which are invariant to changes in geometry and applicable across multiple shape representations. We generate simplified shape graphs by jointly decomposing the…

As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across…