Related papers: A new hybrid genetic algorithm for protein structu…
This paper provides experimental experiences on two local search hybridized genetic algorithms in solving the uncapacitated examination timetabling problem. The proposed two hybrid algorithms use partition and priority based solution…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
We present a scalable combinatorial algorithm for globally optimizing over the space of geometrically consistent mappings between 3D shapes. We use the mathematically elegant formalism proposed by Windheuser et al. (ICCV 2011) where 3D…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
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…
This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
The properties of lattice-based structures can be enhanced by varying their geometric parameters in a graded manner, and the gradation can be tailored to extremize a particular objective. In this manuscript, we propose a non-gradient-based…
This study presents a hybrid metaheuristic for the resource-constrained project scheduling problem (RCPSP), which integrates a genetic algorithm (GA) and a neighborhood search strategy (NS). The RCPSP consists of a set of activities that…
We review algorithms for protein design in general. Although these algorithms have a rich combinatorial, geometric, and mathematical structure, they are almost never covered in computer science classes. Furthermore, many of these algorithms…
Packing problems are in general NP-hard, even for simple cases. Since now there are no highly efficient algorithms available for solving packing problems. The two-dimensional bin packing problem is about packing all given rectangular items,…
Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…
A hybrid evolutionary algorithm with importance sampling method is proposed for multi-dimensional optimization problems in this paper. In order to make use of the information provided in the search process, a set of visited solutions is…
This paper presents a parallel genetic algorithm for three dimensional bin packing with heterogeneous bins using Hadoop Map-Reduce framework. The most common three dimensional bin packing problem which packs given set of boxes into minimum…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and…
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…
The Molecular Distance Geometry Problem (MDGP) is essential in structural biology, as it seeks to determine three-dimensional protein structures from partial interatomic distances. Its discretizable subclass (DMDGP) admits an exact…
Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein…
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)…