Related papers: Recent Advances in Solving the Protein Threading P…
The prize-collecting Steiner tree problem PCSTP is a well-known generalization of the classical Steiner tree problem in graphs, with a large number of practical applications. It attracted particular interest during the latest (11th) DIMACS…
We present a novel method for the automatic detection of pockets on protein molecular surfaces. The algorithm is based on an ad hoc hierarchical clustering of virtual SES probe spheres obtained from the geometrical primitives generated by…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
Table structure recognition is a crucial part of document image analysis domain. Its difficulty lies in the need to parse the physical coordinates and logical indices of each cell at the same time. However, the existing methods are…
We study the problem of efficiently clustering protein sequences in a limited information setting. We assume that we do not know the distances between the sequences in advance, and must query them during the execution of the algorithm. Our…
Non-differentiable and constrained optimization play a key role in machine learning, signal and image processing, communications, and beyond. For high-dimensional minimization problems involving large datasets or many unknowns, the…
The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
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…
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…
Parameter-efficient fine-tuning (PEFT) methods have emerged as a practical solution for adapting large foundation models to downstream tasks, reducing computational and memory costs by updating only a small subset of parameters. Among them,…
Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein-protein interaction…
Compressed sensing has shown great potentials in accelerating magnetic resonance imaging. Fast image reconstruction and high image quality are two main issues faced by this new technology. It has been shown that, redundant image…
Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary…
How can we design protein sequences folding into the desired structures effectively and efficiently? AI methods for structure-based protein design have attracted increasing attention in recent years; however, few methods can simultaneously…
Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum clique problems in specific k-partite…
We present a novel hierarchical formulation of the fourth-order forward symplectic integrator and its numerical implementation in the GPU-accelerated direct-summation N-body code FROST. The new integrator is especially suitable for…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
Protein folding is a central challenge in computational biology, with important applications in molecular biology, drug discovery and catalyst design. As a hard combinatorial optimisation problem, it has been studied as a potential target…