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Ab Initio Protein Structure Prediction Using Evolutionary Approach: A Survey

Lucas Siqueira, Sandra Venske
2021 Revista de Informática Teórica e Aplicada  
In this paper, we present a survey on methods to approach the \textit{ab initio} protein structure prediction based on evolutionary computing algorithms, considering both single and multi-objective optimization  ...  Thus, the knowledge of the structure and functionality of proteins, combined with the prediction of their structure is a complex problem and a challenge for the area of computational biology.  ...  Genetic Algorithms of ab initio off-lattice protein structure prediction. the balance and stability of a structure. The representation used was the full-atom torsion angle.  ... 
doi:10.22456/2175-2745.111993 fatcat:a4pzedhyivf2hgnk6ixrr5bxzy

Multi-Objective Approach in Predicting Amino Acid Interaction Network Using Ant Colony Optimization

Md. Shiplu Hawlader, Saifuddin Md. Tareeq
2014 International Journal of Artificial Intelligence & Applications  
In this paper we have formalized amino acid interaction network prediction as a multi-objective evolutionary optimization problem.  ...  This problem is then solved and implemented using multi-objective genetic algorithm and subsequently optimized using ant colony optimization technique.  ...  The multi-objective optimization algorithm will predict structural motifs of a protein and will give a network or graph of secondary structural element (SSE) of the protein.  ... 
doi:10.5121/ijaia.2014.5109 fatcat:7fy7zg2iprbppkwollw3wmbfee

Amino Acid Interaction Network Prediction using Multi-objective Optimization [article]

Md. Shiplu Hawlader, Saifuddin Md. Tareeq
2014 arXiv   pre-print
In this paper we present a multi-objective evolutionary algorithm for interaction prediction and ant colony probabilistic optimization algorithm is used to confirm the interaction.  ...  This interaction network is the first step of proteins three-dimensional structure prediction.  ...  The multi-objective optimization algorithm will predict structural motifs of a protein and will give a network or graph of secondary structural element (SSE) of the protein.  ... 
arXiv:1401.3446v1 fatcat:nda4zkktxfa3hi7ngat3d77a24

A Survey of Protein Fold Recognition Algorithms

Mohammed Said Abual-Rub, Rosni Abdullah
2008 Journal of Computer Science  
Approach: We reviewed various algorithms that have been developed for protein structure prediction by threading and fold recognition.  ...  Problem statement: Predicting the tertiary structure of proteins from their linear sequence is really a big challenge in biology.  ...  algorithm paradigm for protein threading The genetic algorithm approach to protein structure A framework of genetic algorithms for protein structure prediction [24] prediction.  ... 
doi:10.3844/jcssp.2008.768.776 fatcat:iqxcwkwe2jeibff4dntd7c6lmm

Multi-objective optimization methods in drug design

Christos A. Nicolaou, Nathan Brown
2013 Drug Discovery Today : Technologies  
Drug discovery is a challenging multi-objective problem where numerous pharmaceutically important objectives need to be adequately satisfied for a solution to be found.  ...  Multi-objective optimization methods, designed specifically to address such problems, have been introduced to the drug discovery field over a decade ago and have steadily gained in acceptance ever since  ...  Acknowledgements CN would like to thank Christine Humblet (Eli Lilly & Co.) for reviewing the manuscript and providing useful feedback. NB is funded by Cancer Research UK Grant no. C309/A8274.  ... 
doi:10.1016/j.ddtec.2013.02.001 pmid:24050140 fatcat:tkaroywsf5dfhmwh7sbi7quoju

GAMMA: a new docking program utilizing an advanced evolution system algorithm as an engine

S. Ness, T. Hart, R. Read
1996 Acta Crystallographica Section A Foundations of Crystallography  
prediction algorithm will still encounter the structural plasticity dilemma.  ...  The cupredoxin fold is found in a fQmily of copper containing proteins that include single domain electTon transfer proteins and multi-domain multi-subunit enzymes that caL"1lyze a vmiety of redox reactions  ...  prediction algorithm will still encounter the structural plasticity dilemma.  ... 
doi:10.1107/s0108767396095499 fatcat:fv4cprjhfrdllohn3wg36acqca

Multi-objective optimization and data analysis in informationization

Kelvin Kian Loong Wong, Zhihua Liu, Quan Zou
2019 Computing  
However, there still are some challenging problems for providing a better service. For most given problems, multi-objective optimization and data mining can provide the optimal solution.  ...  And machine learning such as artificial neural network, deep learning, evolutionary algorithm, and genetic algorithm are some of the other well-established techniques we can explore for solutions generation  ...  The obtained results demonstrate that multi-objective simulated annealing algorithm has better efficiency in small-sized problems and non-dominated sorting genetic algorithm II in large-sized problems.  ... 
doi:10.1007/s00607-019-00718-3 fatcat:g2wo6hlgeffizapbzvjslsfps4

The characteristics of common sequence peptides in proteins

L. Lai, D. Lin, Y. Tang
1996 Acta Crystallographica Section A Foundations of Crystallography  
prediction algorithm will still encounter the structural plasticity dilemma.  ...  The cupredoxin fold is found in a fQmily of copper containing proteins that include single domain electTon transfer proteins and multi-domain multi-subunit enzymes that caL"1lyze a vmiety of redox reactions  ...  prediction algorithm will still encounter the structural plasticity dilemma.  ... 
doi:10.1107/s0108767396095517 fatcat:itnt6l5bffeobfmvrqfjihzw5y

The cupredoxin fold: definition and analysis of the common core structure

M. E. P. Murphy, E. T. Adman
1996 Acta Crystallographica Section A Foundations of Crystallography  
prediction algorithm will still encounter the structural plasticity dilemma.  ...  The cupredoxin fold is found in a fQmily of copper containing proteins that include single domain electTon transfer proteins and multi-domain multi-subunit enzymes that caL"1lyze a vmiety of redox reactions  ...  prediction algorithm will still encounter the structural plasticity dilemma.  ... 
doi:10.1107/s0108767396095505 fatcat:4vpnz5gcvnfapbavvtbg27oscu

Modes of binding synthetic inhibitors to factor Xa: an automated docking approach

M. S. Rao, A. J. Olson
1996 Acta Crystallographica Section A Foundations of Crystallography  
prediction algorithm will still encounter the structural plasticity dilemma.  ...  The cupredoxin fold is found in a fQmily of copper containing proteins that include single domain electTon transfer proteins and multi-domain multi-subunit enzymes that caL"1lyze a vmiety of redox reactions  ...  prediction algorithm will still encounter the structural plasticity dilemma.  ... 
doi:10.1107/s0108767396095487 fatcat:jjhrojlkdbg2llbzrjksbwtf2m

Multi-objective optimisation of the protein-ligand docking problem in drug discovery

A. Oduguwa, A. Tiwari, S. Fiorentino, R. Roy
2006 Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06  
This paper explores the application of evolutionary multi-objective optimisation techniques for achieving such predictive work in protein-ligand docking.  ...  The paper reviews the literature of multi-objective optimisation and the drug discovery process and proposes a framework as a predictive tool to calculate good docking configuration for a given target  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge the support of the Engineering and Physical Research Council (EPSRC) and the Centre for Decision Engineering at Cranfield University, UK.  ... 
doi:10.1145/1143997.1144287 dblp:conf/gecco/OduguwaTFR06 fatcat:pc3cwxljdjcydni6azdwfaz3ji

Improving the Efficiency of MECoMaP: A Protein Residue-Residue Contact Predictor [chapter]

Alfonso E. Márquez Chamorro, Federico Divina, Jesús S. Aguilar-Ruiz, Cosme E. Santiesteban Toca
2013 Lecture Notes in Computer Science  
This work proposes an improvement of the multi-objective evolutionary method for the protein residue-residue contact prediction called MECoMaP.  ...  This method bases its prediction on physicochemical properties of amino acids, structural features and evolutionary information of the proteins.  ...  Conclusions and Future Work In this work, we presented some improvements to a multi-objective optimization algorithm for the residue-residue contact prediction.  ... 
doi:10.1007/978-3-642-41827-3_21 fatcat:gvrasfysdnaclcmhjyhunfass4

A Randomized Clustering Forest Approach for Efficient Prediction of Protein Functions

Hong Tang, Yuanyuan Wang, Shaomin Tang, Dianhui Chu, Chunshan Li
2019 IEEE Access  
In this paper, we propose a novel ensemble MIML algorithm called multi-instance multi-label randomized clustering forest (MIMLRC-Forest) for protein function prediction.  ...  Then, the label dependency can be computed by aggregating tree labels for protein function prediction.  ...  Moreover, the proposed MIMLRC-Forest algorithm can provide a target for genetic manipulation and a reliable basis for designing new proteins or modifying existing ones.  ... 
doi:10.1109/access.2019.2892120 fatcat:g2uxcgfhfjcp7dsaxrbiooibuu

Page 22 of The Journal of the Operational Research Society Vol. 58, Issue 1 [page]

2007 The Journal of the Operational Research Society  
Genetic algorithms using multi-objectives in a multi-agent system. Robot Autono- mous Syst 33: 179-190. Carvalho MT and Durao F (2002). Control of a flotation column using fuzzy logic inference.  ...  A genetic algorithm for scheduling staff of mixed skills under multi-criteria. Eur J Opl Res 125: 359-369. ‘ai YD, Yu H and Chou KC (1998).  ... 

Neural networks and genetic algorithms in drug design

L TERFLOTH
2001 Drug Discovery Today  
We then go on to give a general outline of genetic algorithms.  ...  Finally, we report the applications of genetic algorithms to structure alignment, variable selection in QSAR studies, structure generation, design of combinatorial libraries, and docking of ligands to  ...  The RMS (root mean square) value is 2.41 Å for the rigid alignment (b) and 0.81 Å for the flexible alignment (c). Schematic view of a genetic algorithm.  ... 
doi:10.1016/s1359-6446(01)00173-8 fatcat:5jt3r4bgfvbe5b6phd4lidln4a
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