Related papers: Maximum Cliques in Protein Structure Comparison
The generation of protein crystals is necessary for the study of protein molecular function and structure. This is done empirically by processing large numbers of crystallization trials and inspecting them regularly in search of those with…
Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and…
As a fundamental problem in computer vision, 3D point cloud registration (PCR) aims to seek the optimal pose to align a point cloud pair. In this paper, we present a 3D registration method with maximal cliques (MAC). The key insight is to…
A \emph{disk graph} is the intersection graph of (closed) disks in the plane. We consider the classic problem of finding a maximum clique in a disk graph. For general disk graphs, the complexity of this problem is still open, but for unit…
While DeepMind has tentatively solved protein folding, its inverse problem -- protein design which predicts protein sequences from their 3D structures -- still faces significant challenges. Particularly, the lack of large-scale standardized…
Finding the clique of maximum cardinality in an arbitrary graph is an NP-Hard problem that has many applications, which has motivated studies to solve it exactly despite its difficulty. The great majority of algorithms proposed in the…
We take an existing implementation of an algorithm for the maximum clique problem and modify it so that we can distribute it over an ad-hoc cluster of machines. Our goal was to achieve a significant speedup in performance with minimal…
In this paper, we provide polynomial-time algorithms for different extensions of the matching counting problem, namely maximal matchings, path matchings (linear forest) and paths, on graph classes of bounded clique-width. For maximal…
The advent of new special-purpose hardware such as FPGA or ASIC-based annealers and quantum processors has shown potential in solving certain families of complex combinatorial optimization problems more efficiently than conventional CPUs.…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in…
Given a set $P$ of $n$ points in the plane, the unit-disk graph $G(P)$ is a graph with $P$ as its vertex set such that two points of $P$ have an edge if their Euclidean distance is at most $1$. We consider the problem of computing a maximum…
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…
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)…
This manuscript provides a comprehensive review of the Maximum Clique Problem, a computational problem that involves finding subsets of vertices in a graph that are all pairwise adjacent to each other. The manuscript covers in a simple way…
We study the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss…
A $k$-defective clique is a relaxation of the traditional clique definition, allowing up to $k$ missing edges. This relaxation is crucial in various real-world applications such as link prediction, community detection, and social network…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
This paper unifies the theory of consistent-set maximization for robust outlier detection in a simultaneous localization and mapping framework. We first describe the notion of pairwise consistency before discussing how a consistency graph…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…