Protein folding in simplified models with estimation of distribution algorithms

R Santana, P Larrañaga… - IEEE transactions on …, 2008 - ieeexplore.ieee.org
Simplified lattice models have played an important role in protein structure prediction and
protein folding problems. These models can be useful for an initial approximation of the …

Protein folding prediction in a cubic lattice in hydrophobic-polar model

N Yanev, M Traykov, P Milanov… - Journal of Computational …, 2017 - liebertpub.com
The tertiary structure of the proteins determines their functions. Therefore, the predicting of
protein's tertiary structure, based on the primary amino acid sequence from long time, is the …

Application of tabu search strategy for finding low energy structure of protein

J Błażewicz, P Łukasiak, M Miłostan - Artificial Intelligence in Medicine, 2005 - Elsevier
OBJECTIVE:: Understanding protein functionality would mean understanding the basics of
life. This functionality follows a three-dimensional structure of proteins. Unfortunately till now …

Emergent protein folding modeled with evolved neural cellular automata using the 3D HP model

J Santos, P Villot, M Diéguez - Journal of Computational Biology, 2014 - liebertpub.com
We used cellular automata (CA) for the modeling of the temporal folding of proteins. Unlike
the focus of the vast research already done on the direct prediction of the final folded …

Memory-based local search for simplified protein structure prediction

S Shatabda, MAH Newton, DN Pham… - Proceedings of the ACM …, 2012 - dl.acm.org
Protein structure prediction is one of the most challenging problems in computational
biology. Given a protein's amino acid sequence, a simplified version of the problem is to find …

An efficient encoding for simplified protein structure prediction using genetic algorithms

S Shatabda, MAH Newton, MA Rashid… - 2013 IEEE Congress …, 2013 - ieeexplore.ieee.org
Protein structure prediction is one of the most challenging problems in computational
biology and remains unsolved for many decades. In a simplified version of the problem, the …

The road not taken: retreat and diverge in local search for simplified protein structure prediction

S Shatabda, MA Hakim Newton, MA Rashid… - BMC …, 2013 - Springer
Background Given a protein's amino acid sequence, the protein structure prediction problem
is to find a three dimensional structure that has the native energy level. For many decades, it …

Some operations research methods for analyzing protein sequences and structures

P Łukasiak, J Błażewicz, M Miłostan - Annals of Operations Research, 2010 - Springer
The operations research is probably one of the most successful field of applied mathematics
used in economics, physics, chemistry, almost everywhere where one has to analyze huge …

Some operations research methods for analyzing protein sequences and structures

J Błażewicz, P Łukasiak, M Miłostan - 4OR, 2006 - Springer
Operations Research is probably one of the most successful fields of applied mathematics
used in Economics, Physics, Chemistry, almost everywhere one has to analyze huge …

[PDF][PDF] Algorithm for protein folding problem in 3D lattice HP model

M Traykov, N Yanev, R Mavrevski… - International Journal of …, 2018 - iaras.org
The prediction of a protein's tertiary structure from the amino acid sequence of a protein is
known as the protein folding problem. The protein folding problem in 3D lattice Hydrophobic …