Related papers: CLeFAPS: Fast Flexible Alignment of Protein Struct…
Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…
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…
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Motivation: Protein sequence world is discrete as 20 amino acids (AA) while its structure world is continuous, though can be discretized into structural alphabets (SA). In order to reveal the relationship between sequence and structure, it…
We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to…
Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…
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…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
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 demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue…
The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…
We introduce a lightweight and accurate architecture for resource-efficient visual correspondence. Our method, dubbed XFeat (Accelerated Features), revisits fundamental design choices in convolutional neural networks for detecting,…
Developing a reliable and practical face recognition system is a long-standing goal in computer vision research. Existing literature suggests that pixel-wise face alignment is the key to achieve high-accuracy face recognition. By assuming a…