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An effective hybrid of hill climbing and genetic algorithm for 2D triangular protein structure prediction

Shih-Chieh Su, Cheng-Jian Lin, Chuan-Kang Ting
2011 Proteome Science  
Methods: This paper proposes a hybrid of hill-climbing and genetic algorithm (HHGA) based on elite-based reproduction strategy for protein structure prediction on the 2D triangular lattice.  ...  The satisfactory simulation results demonstrate the effectiveness of the proposed HHGA and the utility of the 2D triangular lattice model for protein structure prediction.  ...  Roy Preece at Oxford Brookes University for the proofreading of the manuscript and Dr. Lihui Wang at Imperial College London for advice on writing of the manuscript.  ... 
doi:10.1186/1477-5956-9-s1-s19 pmid:22166054 pmcid:PMC3289079 fatcat:che7owmkzfc43hu5oh5rc6bjdq

Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm

Cheng-Hong Yang, Kuo-Chuan Wu, Yu-Shiun Lin, Li-Yeh Chuang, Hsueh-Wei Chang
2018 BioData Mining  
Conclusion: Overall, the HP model integrated with IMO and a greedy algorithm as IMOG provides an improved way of protein structure prediction of high stability, high efficiency, and outstanding performance  ...  Results: In this study, the ions motion optimization (IMO) algorithm was combined with the greedy algorithm (namely IMOG) and implemented to the HP model for the protein folding prediction based on the  ...  Availability of data and materials The dataset of amino acids sequences in HP model used in this study was mentioned in Tables 1 and 2 with citing the references [9, 21] .  ... 
doi:10.1186/s13040-018-0176-6 pmid:30116298 pmcid:PMC6083565 fatcat:usqkuh7y6ncprjefpntawjarlq

Enhanced Genetic Algorithm for Protein Structure Prediction based on the HP Model [chapter]

Nashat Mansour, Fatima Kanj, Hassan Khachfe
2011 Search Algorithms and Applications  
Results for sequences of length 64 Enhanced Genetic Algorithm for Protein Structure Prediction based on the HP Model Proposed EGA Patton et al.  ...  In this paper, we present a genetic algorithm for the protein structure prediction problem based on the cubic 3D hydrophobic polar (HP) model.  ...  Enhanced Genetic Algorithm for Protein Structure Prediction based on the HP Model, Search Algorithms and Applications, Prof.  ... 
doi:10.5772/15796 fatcat:l3hqcmdewjcq7bsaaljzvlotza

MAS2HP: A Multi Agent System to Predict Protein Structure in 2D HP model [article]

Hossein Parineh, Nasser Mozayani
2022 arXiv   pre-print
Protein Structure Prediction (PSP) is an unsolved problem in the field of computational biology.  ...  In this paper we proposed a new approach for protein structure prediction by using agent-based modeling (ABM) in two dimensional hydrophobic-hydrophilic model.  ...  Energy Function To assess algorithm effectiveness in different methods and models, final energy of the predicted structure is compared. In this work, we use 2D HP lattice model.  ... 
arXiv:2205.08451v4 fatcat:2qbohq5omndcdeegmxedht3ggi

Criterion based Two Dimensional Protein Folding Using Extended GA

T Kalaichelvi
2012 International Journal of Computer Science Engineering and Information Technology  
Moreover, the model incorporates Extended Genetic Algorithm (EGA) with concealed Markov model (CMM) for effectively folding the protein sequences that are having long chain lengths.  ...  With that consideration, this paper contributes to the protein folding research field and presents a novel procedure for mapping appropriate protein structure to its correct 2D fold by a concrete model  ...  The algorithm replaced the traditional fitness function of HP model with the composite fitness function to enhance the prediction performance.  ... 
doi:10.5121/ijcseit.2012.2507 fatcat:t7ka5j6nd5fshc7lpq6at6grlq

A Hybrid Genetic Algorithm for 2D Protein Folding Simulations

Hamza Turabieh
2016 International Journal of Computer Applications  
Protein folding is NP hard problem. In this paper, we hybridized genetic algorithm with a local search algorithm to solve 2D Protein folding problem.  ...  Protein folding problem is one of the most interesting problem in the medical field, which consists in finding the tertiary structure for a given amino acid sequence of a protein.  ...  Section 2 describes 2D HP model for protein folding. Section 3 illustrates Genetic Algorithm, great deluge algorithms and the hybrid algorithms used to solve 2D HP model.  ... 
doi:10.5120/ijca2016909127 fatcat:4pp76msawfh3fn33d4vtfu43qu

Solving Two-Dimensional HP Model by Firefly Algorithm and Simplified Energy Function

Yudong Zhang, Lenan Wu, Shuihua Wang
2013 Mathematical Problems in Engineering  
It concludes that it is effective to solve 2D HP model by the firefly algorithm and the simplified energy function.  ...  In order to solve the HP model of the protein folding problem, we investigated traditional energy function and pointed out that its discrete property cannot give direction of the next step to the searching  ...  Scholars tend to use the 2D lattice model (HP model) for protein folding. The HP model was proposed by Lau and Dill [7] .  ... 
doi:10.1155/2013/398141 fatcat:5odcjdb6tbdnhmgswwlh7ofriy

Enhanced Population Based Ant Colony For The 3D Hydrophobic Polar Protein Structure Prediction Problem

Abdel-Rahman Hedar2 and Marghny. H. Mohammed3 Sara Salah1
2013 Zenodo  
KEYWORDS Population based ACO, Ant Colony Optimization, HP Model, Protein Structure Prediction 1.  ...  The protein structure prediction problem (PSP) is that of computationally predicting the three dimensional structure of protein from the sequence of amino acids alone. This has been a [...]  ...  The performance of the proposed model is compared to the best results obtained by other algorithms for protein structure prediction in 3D HP model.  ... 
doi:10.5281/zenodo.1402500 fatcat:qjq26ds7bzat3apfhaqp6eid5q

A New Genetic Algorithm for Simplified Protein Structure Prediction [chapter]

Mahmood A. Rashid, Md. Tamjidul Hoque, M. A. Hakim Newton, Duc Nghia Pham, Abdul Sattar
2012 Lecture Notes in Computer Science  
In this paper, we present a new genetic algorithm for protein structure prediction problem using face-centred cubic lattice and hydrophobic-polar energy model.  ...  On a set of standard benchmark proteins, our algorithm significantly outperforms the state-of-the-art algorithms for the same models.  ...  Acknowledgments NICTA is funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council through the ICT Centre  ... 
doi:10.1007/978-3-642-35101-3_10 fatcat:kh45qnj75jd3nlfctateixcip4

Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction

Camelia Chira, Dragos Horvath, D Dumitrescu
2011 BioData Mining  
An evolutionary model based on hillclimbing genetic operators is proposed for protein structure prediction in the hydrophobic -polar (HP) model.  ...  The protein structure prediction problem is NP-hard even in simplified lattice protein models.  ...  Acknowledgements This research is supported by Grant PN II TE 320/2010, Emergence, auto-organization and evolution: New computational models in the study of complex systems, funded by CNCS Romania.  ... 
doi:10.1186/1756-0381-4-23 pmid:21801435 pmcid:PMC3161899 fatcat:4lfzlik2rndebpk3c4kkj3b6zy

Protein folding simulations in the hydrophobic-polar model using a hybrid cuckoo search algorithm [article]

Nabil Boumedine, Sadek Bouroubi
2021 arXiv   pre-print
In this paper, we present a new Hybrid Cuckoo Search Algorithm (HCSA) to solve the 3D-HP protein folding optimization problem.  ...  The principal challenge of PFP is to predict the optimal conformation of a given protein by considering only its amino acid sequence.  ...  in different types of lattices in the 2D-HP and 3D-HP model that can predict well-approximated conformations for the real proteins.  ... 
arXiv:2105.13226v1 fatcat:ypzq4mhoo5hdvd6h6wvjcmwo24

An effective evolutionary algorithm for protein folding on 3D FCC HP model by lattice rotation and generalized move sets

Jyh-Jong Tsay, Shih-Chieh Su
2013 Proteome Science  
In the past, the HP lattice model was one of the ab initio methods that many researchers used to forecast the protein structure.  ...  The model has been employed to investigate general principles of protein folding, and plays an important role in the prediction of protein structures.  ...  Declarations The publication costs for this article were funded by the authors.  ... 
doi:10.1186/1477-5956-11-s1-s19 pmid:24565217 pmcid:PMC3908773 fatcat:fup3sh7xzjdtjak7bmsj4pzxta

A Parallel Framework for Multipoint Spiral Search inab InitioProtein Structure Prediction

Mahmood A. Rashid, Swakkhar Shatabda, M. A. Hakim Newton, Md Tamjidul Hoque, Abdul Sattar
2014 Advances in Bioinformatics  
In ourab initioprotein structure prediction method, we use the three-dimensional face-centred-cubic lattice for structure-backbone mapping.  ...  Protein structure prediction is computationally a very challenging problem.  ...  Acknowledgments The authors would like to express their great appreciation to the people managing the Cluster Computing Services at National ICT Australia (NICTA) and Griffith University. Md Tamjidul  ... 
doi:10.1155/2014/985968 pmid:24744779 pmcid:PMC3976798 fatcat:3ozeocfgjbfy3puxabitu2winu

Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding [chapter]

Gabriela Ochoa, Gabi Escuela, Natalio Krasnogor
2006 Lecture Notes in Computer Science  
The ability of this encoding to capture protein native conformations was tested using an evolutionary algorithm as the inference procedure for discovering L-systems.  ...  An encoding scheme for protein folding on lattice models, inspired by parametric L-systems, was proposed.  ...  Acknowledgements Natalio Krasnogor acknowledges EPSRC (GR/T07534/01, EP/D021847/1) and BBSRC (BB/C511764/1) for funding his research on protein structure prediction, comparison and self-assembly  ... 
doi:10.1007/11740698_22 fatcat:mckmpz3xavhdbicsuaiqnrajpi

Search Strategies in Structural Bioinformatics

Mark Oakley, Daniel Barthel, Yuri Bykov, Jonathan Garibaldi, Edmund Burke, Natalio Krasnogor, Jonathan Hirst
2008 Current protein and peptide science  
In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the  ...  We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm.  ...  Acknowledgments We are grateful for access to the University of Nottingham's high performance computer and for financial support from EPSRC (GR/T07534/01), BBSRC (grant BB/C511764/1) and the EU (NoE BIOPATTERN  ... 
doi:10.2174/138920308784534032 pmid:18537681 fatcat:2tptsm5v2recdmlorrt5c7i7k4
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