Related papers: Solving Maximum Clique Problem for Protein Structu…
A rectangle blanket is a set of non-overlapping axis-aligned rectangles, used to approximately represent the two dimensional image of a shape approximately. The use of a rectangle blanket is a widely considered strategy for speeding-up the…
Finding a Maximum Clique is a classic property test from graph theory; find any one of the largest complete subgraphs in an Erd\"os-R\'enyi G(N, p) random graph. We use Maximum Clique to explore the structure of the problem as a function of…
The comparison of protein structures is a fundamental task in computational biology, crucial for understanding protein function, evolution, and for drug design. While analytical methods like the Kabsch algorithm provide an exact,…
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
In this paper we report on an algorithm for aligning multiple protein structures. The algorithm has been tested on a variety of inputs and it performs well in comparison to well-known algorithms for this problem.
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…
Bipartite Correlation clustering is the problem of generating a set of disjoint bi-cliques on a set of nodes while minimizing the symmetric difference to a bipartite input graph. The number or size of the output clusters is not constrained…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
Finding maximum cliques in large networks is a challenging combinatorial problem with many real-world applications. We present a fast algorithm to achieve the exact solution for the maximum clique problem in large sparse networks based on…
In this paper, we consider the planted quasi-clique or {\gamma}-clique problem. This problem is an extension of the well known planted clique problem which is NP-hard. The maximum quasi-clique problem is applicable in community detection,…
Biclustering techniques have been widely used to identify homogeneous subgroups within large data matrices, such as subsets of genes similarly expressed across subsets of patients. Mining a max-sum sub-matrix is a related but distinct…
The flawless functioning of a protein is essentially linked to its own three-dimensional structure. Therefore, the prediction of a protein structure from its amino acid sequence is a fundamental problem in many fields that draws researchers…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
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…
Accurately predicting protein structures from amino acid sequences remains a fundamental challenge in computational biology, with profound implications for understanding biological functions and enabling structure-based drug discovery.…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
Non-overlapping codes are block codes that have arisen in diverse contexts of computer science and biology. Applications typically require finding non-overlapping codes with large cardinalities, but the maximum size of non-overlapping codes…
To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D…
Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…