Related papers: A new hybrid genetic algorithm for protein structu…
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…
Surface registration is a technique that is used in various areas such as object recognition and 3D model reconstruction. Problem of surface registration can be analyzed as an optimization problem of seeking a rigid motion between two…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
Much recent research has been conducted in the area of Bayesian learning, particularly with regard to the optimization of hyper-parameters via Gaussian process regression. The methodologies rely chiefly on the method of maximizing the…
Genetic algorithms (GAs) have a long history of over four decades. GAs are adaptive heuristic search algorithms that provide solutions for optimization and search problems. The GA derives expression from the biological terminology of…
Structure-based drug design (SBDD) leverages the three-dimensional geometry of proteins to identify potential drug candidates. Traditional approaches, rooted in physicochemical modeling and domain expertise, are often resource-intensive.…
In this paper, a novel knowledge-based genetic algorithm for path planning of a mobile robot in unstructured complex environments is proposed, where five problem-specific operators are developed for efficient robot path planning. The…
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…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
The protein backbone is described as a smooth curved and twisted line in three-dimensional (3D) space and characterized by its curvature $\kappa(s)$ and torsion $\tau(s)$ both expressed as a function of arc length s. It is shown that the…
Motivation: Discovering functional modules in protein-protein interaction (PPI) networks by optimization methods remains a longstanding challenge in biology. Traditional algorithms simply consider strong protein complexes that can be found…
We examined what determines the designability of 2-letter codes (H and P) lattice proteins from three points of view. First, whether the native structure is searched within all possible structures or within maximally compact structures.…
Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying…
This article presents a generic method to solve 2D multi-objective placement problem for free-form components. The proposed method is a relaxed placement technique combined with an hybrid algorithm based on a genetic algorithm and a…
The genetic algorithm is an optimization procedure motivated by biological evolution and is successfully applied to optimization problems in different areas. A statistical mechanics model for its dynamics is proposed based on the…
We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing…
Analyzing large datasets to select optimal features is one of the most important research areas in machine learning and data mining. This feature selection procedure involves dimensionality reduction which is crucial in enhancing the…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
Higher-dimensional orthogonal packing problems have a wide range of practical applications, including packing, cutting, and scheduling. Previous efforts for exact algorithms have been unable to avoid structural problems that appear for…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…