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RNA folding on the 3D triangular lattice

Joel Gillespie, Martin Mayne, Minghui Jiang
2009 BMC Bioinformatics  
Protein folding, for example, has long been studied in the lattice model. Recently, researchers have also begun to apply the lattice model to the study of RNA folding.  ...  We present a novel method for predicting RNA secondary structures with pseudoknots: first simulate the folding dynamics of the RNA sequence on the 3D triangular lattice, next extract and select a set of  ...  Neff for his help in extracting pseudoknot data from PseudoBase [14] . We thank Yuguang Zeng for his help in acquiring stacking pair energy parameters from Mfold [21, 22] .  ... 
doi:10.1186/1471-2105-10-369 pmid:19891777 pmcid:PMC2780420 fatcat:ctuyylqdofebrecsc4vfuuxe7u

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  
From visual comparison, it was found that a 2D triangular lattice model can give a better structure modeling and prediction for proteins with short primary amino acid sequences.  ...  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

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  
We propose to combine three different local search methods, including lattice rotation for crossover, Ksite move for mutation, and generalized pull move; these form our key components to improve previous  ...  Methods: In this paper, we present an improved evolutionary algorithm for the protein folding problem.  ...  Lihui Wang at Imperial College London for advice on writing the manuscript and Dr. Roy Preece at Oxford Brookes University for proofreading.  ... 
doi:10.1186/1477-5956-11-s1-s19 pmid:24565217 pmcid:PMC3908773 fatcat:fup3sh7xzjdtjak7bmsj4pzxta

On the Characterization and Software Implementation of General Protein Lattice Models

Alessio Bechini, Freddie Salsbury
2013 PLoS ONE  
In this paper, a new general parametric lattice model for simplified protein conformations is proposed and investigated.  ...  Simulations give insights on the use of square and triangular lattices in a range of dimensions.  ...  Insights from Build-up Methods Chain-growth algorithms represent a group of simple yet significant methods for protein folding in a lattice model [48] .  ... 
doi:10.1371/journal.pone.0059504 pmid:23555684 pmcid:PMC3612044 fatcat:waylcmswmrfurpf5bt7zdyieb4

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  
2D-triangular-lattice model.  ...  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

Page 2703 of Mathematical Reviews Vol. , Issue 98D [page]

1998 Mathematical Reviews  
We present a set of folding rules for a triangular lattice and analyze the approx- imation ratio which these rules achieve.  ...  Biology 3 (1996), no. 1, 53-96] gave approxima- tion algorithms for folding proteins on the cubic lattice under the HP model.  ... 

A New Hybrid Genetic Algorithm for Protein Structure Prediction on the 2D Triangular Lattice

2020 Turkish Journal of Electrical Engineering and Computer Sciences  
The Protein Structure Prediction problem (PSP) can be formulated as a combinatorial optimization 6 problem based on simplified lattice models such as the hydrophobic-polar model.  ...  Therefore, 4 predicting protein structure from its amino acid sequence is a fundamental problem that draws researchers' attention 5 in many areas.  ...  Improving genetic algorithms for protein folding simulations by systematic crossover. BioSystems, 50(1):17-25, 1999. move set for protein folding in triangular lattice models.  ... 
doi:10.3906/elk-1909-31 fatcat:did72vbmlnajxgqqycovbxcnqe

Protein Folding Simulation by Two-Stage Optimization [chapter]

A. Dayem Ullah, L. Kapsokalivas, M. Mann, K. Steinhöfel
2009 Communications in Computer and Information Science  
We propose a two-stage optimization approach for protein folding simulation in the FCC lattice, inspired from the phenomenon of hydrophobic collapse.  ...  prediction in the HP model.  ...  It employs the simulated annealing algorithm with the pull-moves for triangular lattices and optimizes a more complex energy function.  ... 
doi:10.1007/978-3-642-04962-0_16 fatcat:w7bp623worgd7nuu7oou32d22u

Multimeme Algorithms for Protein Structure Prediction [chapter]

N. Krasnogor, B. P. Blackburne, E. K. Burke, J. D. Hirst
2002 Lecture Notes in Computer Science  
New benchmark sequences for the triangular lattice in the HP model and Functional Model Proteins in two and three dimensions are included here with their known optima.  ...  As there is no favourite protein model nor exact energy potentials to describe proteins, robustness accross a range of models must be present in any putative structure prediction algorithm.  ...  In this paper we will present a novel metaheuristic, called a Multimeme Algorithm, to PSP for four different models: HP model in the square lattice, HP modelin the triangular lattice, Functional Model  ... 
doi:10.1007/3-540-45712-7_74 fatcat:6apxngxnknblloxz3vbijvrwim

A Novel Framework for Ab Initio Coarse Protein Structure Prediction

Sandhya Parasnath Dubey, S. Balaji, N. Gopalakrishna Kini, M. Sathish Kumar
2018 Advances in Bioinformatics  
The developed framework builds the protein conformation on the square and triangular lattice.  ...  Hydrophobic-Polar model is a simplified representation of Protein Structure Prediction (PSP) problem. However, even with the HP model, the PSP problem remains NP-complete.  ...  Balaji acknowledges the Karnataka Science and Technology Promotion Society (KSTePS), India, for supporting the Centre for Interactive Biomolecular 3D-Literacy (C-in-3D) under the VGST scheme-Centres of  ... 
doi:10.1155/2018/7607384 pmid:30026759 pmcid:PMC6031167 fatcat:s3ymxknbvrb2pbdlkpfabcbpyu

Characterization and Construction of a Family of Highly Symmetric Spherical Polyhedra with Application in Modeling Self-Assembling Structures [article]

Muhibur Rasheed, Chandrajit Bajaj
2015 arXiv   pre-print
In this paper, we formalize the necessary and sufficient conditions for symmetric assembly using exactly one type of building block.  ...  However, they only represent a small number of possible spherical layouts which can serve as templates for symmetric assembly.  ...  For example, in Figure 3 (b), A, B and C are locations of 5-fold global symmetry and D is a location of 3-fold local symmetry.  ... 
arXiv:1507.08374v1 fatcat:u2mp2jdtcbanvmsomq72fsiaz4

Protein Folding in the Hexagonal Prism Lattice with Diagonals [article]

Dipan Lal Shaw, M. Sohel Rahman, A. S. M. Sohidull Islam, Shuvasish Karmaker
2014 arXiv   pre-print
We give two approximation algorithm for protein folding on this lattice. Our first algorithm leads us to similar structure of helix structure which is commonly found in protein structure.  ...  Since, it is a problem of great potential complexity many simplified energy model have been proposed in literature on basis of interaction of amino acid residue in protein.  ...  On the other hand this lattice model remove some well known problems of protein folding in SC lattice e.g., parity problem.  ... 
arXiv:1407.4650v1 fatcat:g2xszgkxb5fszpfkn7vfshhera

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  ...  In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled.  ...  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

PREDICTION OF RESIDUE EXPOSURE AND CONTACT NUMBER FOR SIMPLIFIED HP LATTICE MODEL PROTEINS USING LEARNING CLASSIFIER SYSTEMS

MICHAEL STOUT, JAUME BACARDIT, JONATHAN D. HIRST, JACEK BLAZEWICZ, NATALIO KRASNOGOR
2006 Applied Artificial Intelligence  
The GAssist LCS classified functional HP model proteins on the 3D diamond lattice as folding or non-folding at 88.3% accuracy, outperforming significantly three out of the four other methods.  ...  The performance of a Learning Classifier System (LCS) applied to the classification of simplified hydrophobic/polar (HP) lattice model proteins was compared to other machine learning (ML) algorithms.  ...  A 3D HP diamond lattice data set used for the Fold/Non-fold experiments (3DFNF), a 3D HP cubic lattice dataset used for the CN and RE experiments (3DCNRE) and a 2D square lattice dataset used for the CN  ... 
doi:10.1142/9789812774118_0085 fatcat:vhlm2n3w4rc6tp72g7me3femhy

Immune Algorithms with Aging Operators for the String Folding Problem and the Protein Folding Problem [chapter]

V. Cutello, G. Morelli, G. Nicosia, M. Pavone
2005 Lecture Notes in Computer Science  
In particular, for the 3D HP model the IA allowed us to find energy minima not found by other evolutionary algorithms described in literature.  ...  Problem in 2D and 3D lattice.  ...  Acknowledgements. we are grateful to the anonymous referees for their valuable comments.  ... 
doi:10.1007/978-3-540-31996-2_8 fatcat:4yty6mjkkzeapcllshwwvbbium
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