Related papers: Maximum Cliques in Protein Structure Comparison
A basic assumption of molecular biology is that proteins sharing close three-dimensional (3D) structures are likely to share a common function and in most cases derive from a same ancestor. Computing the similarity between two protein…
We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The…
The maximum clique problem is a well known NP-Hard problem with applications in data mining, network analysis, information retrieval and many other areas related to the World Wide Web. There exist several algorithms for the problem with…
We propose a fast, parallel maximum clique algorithm for large sparse graphs that is designed to exploit characteristics of social and information networks. The method exhibits a roughly linear runtime scaling over real-world networks…
Reducing the running time of graph algorithms is vital for tackling real-world problems such as shortest paths and matching in large-scale graphs, where path information plays a crucial role. To address this critical challenge, this paper…
A $k$-defective clique of an undirected graph $G$ is a subset of its vertices that induces a nearly complete graph with a maximum of $k$ missing edges. The maximum $k$-defective clique problem, which asks for the largest $k$-defective…
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…
Link streams offer a good model for representing interactions over time. They consist of links $(b,e,u,v)$, where $u$ and $v$ are vertices interacting during the whole time interval $[b,e]$. In this paper, we deal with the problem of…
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…
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…
Finding complete subgraphs in a graph, that is, cliques, is a key problem and has many real-world applications, e.g., finding communities in social networks, clustering gene expression data, modeling ecological niches in food webs, and…
A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based…
A popular paradigm for 3D point cloud registration is by extracting 3D keypoint correspondences, then estimating the registration function from the correspondences using a robust algorithm. However, many existing 3D keypoint techniques tend…
We propose a family of very efficient hierarchical indexing schemes for ungapped, score matrix-based similarity search in large datasets of short (4-12 amino acid) protein fragments. This type of similarity search has importance in both…
Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring…
A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained attention during past decade because it offers a fine…
The Basic Local Alignment Search Tool (BLAST) is currently the most popular method for searching databases of biological sequences. BLAST compares sequences via similarity defined by a weighted edit distance, which results in it being…
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…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…