相关论文: SHREC 2025: Protein surface shape retrieval includ…

As the usage of 3D models increases, so does the importance of developing accurate 3D shape retrieval algorithms. A common approach is to calculate a shape descriptor for each object, which can then be compared to determine two objects'…

Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…

Over the last few years, several computational techniques have been devised to recover protein complexes from the protein interaction (PPI) networks of organisms. These techniques model "dense" subnetworks within PPI networks as complexes.…

A robust two-stage shape retrieval (TSR) method is proposed to address the 2D shape retrieval problem. Most state-of-the-art shape retrieval methods are based on local features matching and ranking. Their retrieval performance is not robust…

The SHApe Recovery from Partial textured 3D scans challenge, SHARP 2020, is the first edition of a challenge fostering and benchmarking methods for recovering complete textured 3D scans from raw incomplete data. SHARP 2020 is organised as a…

Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…

3D models of humans are commonly used within computer graphics and vision, and so the ability to distinguish between body shapes is an important shape retrieval problem. We extend our recent paper which provided a benchmark for testing…

An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is…

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…

Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which predicts contacts by…

Understanding the semiconductor-electrolyte interface in photoelectrochemical (PEC) systems is crucial for optimizing stability and reactivity. Despite the challenges in establishing reliable surface structure models during PEC cycles, this…

Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…

Protein function is executed at the molecular surface, where shape and chemistry act together to govern interaction. Yet most comparison methods treat these aspects separately, privileging either global fold or local descriptors and missing…

While offering unprecedented resolution of atomic and electronic structure, Scanning Probe Microscopy techniques have found greater challenges in providing reliable electrostatic characterization at the same scale. In this work, we…

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the…

Closed-form, analytical approximations for electrostatic properties of molecules are of unique value, as these can provide computational speed, versatility, and physical insight. Here, we derive a simple, closed-form formula for the…

Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…

The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…

The ensemble average of physical properties of molecules is closely related to the distribution of molecular conformations, and sampling such distributions is a fundamental challenge in physics and chemistry. Traditional methods like…

Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…