Related papers: Towards Reliable Automatic Protein Structure Align…
Aligning partially overlapping point sets where there is no prior information about the value of the transformation is a challenging problem in computer vision. To achieve this goal, we first reduce the objective of the robust point…
Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node "similarities" to rapidly identify from possible alignments the "high-scoring" alignments with respect to the…
Multi-frame human pose estimation has long been a compelling and fundamental problem in computer vision. This task is challenging due to fast motion and pose occlusion that frequently occur in videos. State-of-the-art methods strive to…
Network alignment, the process of finding correspondences between nodes in different graphs, has many scientific and industrial applications. Existing unsupervised network alignment methods find suboptimal alignments that break up node…
Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and…
Graph alignment, which aims at identifying corresponding entities across multiple networks, has been widely applied in various domains. As the graphs to be aligned are usually constructed from different sources, the inconsistency issues of…
Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring…
Interpolation methodologies have been widely used within the domain of indoor positioning systems. However, existing indoor positioning interpolation algorithms exhibit several inherent limitations, including reliance on complex…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Despite considerable progress, ab initio protein structure prediction remains suboptimal. A crowdsourcing approach is the online puzzle video game Foldit, that provided several useful results that matched or even outperformed…
Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or conformational traps reflecting topological frustration…
Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents…
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…
The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…
For many membrane proteins the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as…
As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…