Related papers: Solving Maximum Clique Problem for Protein Structu…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
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 paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
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…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
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…
This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching…
The maximum clique problem finds applications in computer vision, bioinformatics, and network analysis, many of which involve the construction of correspondence graphs to find similarities between two given objects. cliquematch is a Python…
One of the most difficult problems difficult problem in systems biology is to discover protein-protein interactions as well as their associated functions. The analysis and alignment of protein-protein interaction networks (PPIN), which are…
Finding cohesive subgraphs in a large graph has many important applications, such as community detection and biological network analysis. Clique is often a too strict cohesive structure since communities or biological modules rarely form as…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
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…
We present combinatorial approximation algorithms for the weighted correlation clustering problem. In this problem, we have a set of vertices and two weight values for each pair of vertices, denoting their difference and similarity. The…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding…
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…
The maximal clique problem, to find the maximally sized clique in a given graph, is classically an NP-complete computational problem, which has potential applications ranging from electrical engineering, computational chemistry,…