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Page 1974 of Cellular and Molecular Life Sciences Vol. 57, Issue 13-14 [page]

2000 Cellular and Molecular Life Sciences  
Poirrette et al. [40] used a genetic algorithm (GA) to detect the best transformation superposing two molecu- lar surfaces.  ...  A recent work [41] adopts another type of algorithm, the neural network, to generate a map of protein sur-  ... 

Novel Methods for Rapid Comparison and Multimeric Protein Complex Fitting for Low-Resolution Electron Microscopy Data

Lee Sael, Juan Esquivel-Rodriguez, Daisuke Kihara
2011 Biophysical Journal  
First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ...  Our method takes advantage of the stochastic nature of genetic algorithms to identify optimal placements for a template helix.  ...  First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ... 
doi:10.1016/j.bpj.2010.12.1962 fatcat:omiqxzzpwbdnrijmq7n3a3pcga

Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search

Tingjun Hou, Junmei Wang, Lirong Chen, Xiaojie Xu
1999 Protein Engineering Design & Selection  
The first stage was to find a set of potential associated sites mainly based on surface complementarity using a genetic algorithm combined with a tabu search.  ...  A genetic algorithm (GA) combined with a tabu search (TA) has been applied as a minimization method to rake the appropriate associated sites for some biomolecular systems.  ...  Materials and methods Genetic algorithm The idea of a genetic algorithm was borrowed from genetics and natural selection.  ... 
doi:10.1093/protein/12.8.639 pmid:10469824 fatcat:ihqmbytw3rclxjwdqnorrrtsly

Scanning Transmission Electron Microscopy of Eukaryotic Cells in Liquid

Niels de Jonge, Madeline J. Dukes, Elizabeth A. Ring, Diana B. Peckys
2011 Biophysical Journal  
First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ...  Our method takes advantage of the stochastic nature of genetic algorithms to identify optimal placements for a template helix.  ...  First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ... 
doi:10.1016/j.bpj.2010.12.1964 fatcat:gnoprzphxbc5rcbre54wjf3lge

Orbweaver: A New Graphical User Interface for Particle Selection in Single-Particle Reconstruction with Cryo-Em

Robert Ezra Langlois, Joachim Frank
2011 Biophysical Journal  
First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ...  Our method takes advantage of the stochastic nature of genetic algorithms to identify optimal placements for a template helix.  ...  First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ... 
doi:10.1016/j.bpj.2010.12.1965 fatcat:7yijo3lzfnd2bar36rnk2qu4dy

Helex: an Evolutionary Tabu Search Strategy for the Identification of Helical Regions in cryo-Electron Microscopy Reconstructions

Mirabela Rusu, Stefan Birmanns
2011 Biophysical Journal  
First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ...  Our method takes advantage of the stochastic nature of genetic algorithms to identify optimal placements for a template helix.  ...  First, we use the 3DZD for rapid comparison for an EM density map of a protein structure to a database of EM data.  ... 
doi:10.1016/j.bpj.2010.12.1963 fatcat:zvh7wxja3nd4zcnj7oqiun4cqa

A Comparative Study of Parallel Metaheuristics for Protein Structure Prediction on the Computational Grid

Alexandru-Adrian Tantar, Nouredine Melab, El-Ghazali Talbi
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
A comparative study of parallel metaheuristics executed in grid environments is proposed, having as case study a genetic algorithm, a simulated annealing algorithm and a random search method.  ...  The algorithms are evaluated using the protein structure prediction problem, the benchmark instances consisting of the tryptophan-cage protein (Brookhaven Protein Data Bank ID 1L2Y) and α-cyclodextrin.  ...  As a comparison, for the α-cyclodextrin, the set of solutions found by genetic algorithm hybridized with the gradient method had an average of 201.37 kcalmol −1 (stdev. 21.82 kcalmol −1 ), with a maximum  ... 
doi:10.1109/ipdps.2007.370439 dblp:conf/ipps/TantarMT07 fatcat:t4kifzds2fgv7lhru27rxr3rvu

Solving the low dimensional Smoluchowski equation with a singular value basis set

Gregory Scott, Martin Gruebele
2010 Journal of Computational Chemistry  
To demonstrate the practicality of our method, we couple Smoluchowsi dynamics with a genetic algorithm to search for free energy surfaces compatible with the multiprobe thermodynamics and temperature jump  ...  We present a propagation method that considerably reduces computational time for a particular class of problems: when the free energy surface suddenly switches by a small amount, and the probability distribution  ...  A genetic algorithm coupled with our singular value Smoluchowski propagation of p optimizes free energy surfaces by comparison with thermodynamic and kinetic experimental data.  ... 
doi:10.1002/jcc.21535 pmid:20652986 fatcat:liyjqn7s6ra7zi7uyz6zxvnenq

A 3D Surface Fitting Layout for Complex Networks Visualization

Laura Broască, Versavia-Maria Ancuşa, Horia Ciocârlie
2020 Studies in Health Technology and Informatics  
This paper proposes a novel method to generate 3D parameterized layouts, by using a function to correlate the Oz axis and biospecific features.  ...  Large datasets visualization, prevalent in Bioinformatics, is a challenging task.  ...  , Fig. 1 . a shows the distribution of nodes alongside the 3D surface in comparison with a Gephi OpenOrd layout (Fig. 1 . b).  ... 
doi:10.3233/shti200570 pmid:32604677 fatcat:7nbuh4dhavgsrhbv25bkj52444

Diagnosis of Ovarian Cancer Using Decision Tree Classification of Mass Spectral Data

Antonia Vlahou, John O. Schorge, Betsy W. Gregory, Robert L. Coleman
2003 Journal of Biomedicine and Biotechnology  
A decision tree, using five protein peaks resulted in an accuracy of 81.5% in the cross-validation analysis and 80%in a blinded set of samples in differentiating the ovarian cancer from the control groups  ...  The objective of this study was to determine if the commercially available classification algorithm biomarker patterns software (BPS), which is based on a classification and regression tree (CART), would  ...  These studies employed different algorithms to analyze the SELDI data, including a genetic algorithm [19] , a decision tree [17, 18] , and a support vector machine algorithm [20] .  ... 
doi:10.1155/s1110724303210032 pmid:14688417 pmcid:PMC521504 fatcat:g3y5mrajlbe4fif73obnu5tdoi

ENPDA: an evolutionary structure-based de novo peptide design algorithm

Ignasi Belda, Sergio Madurga, Xavier Llorà, Marc Martinell, Teresa Tarragó, Mireia G. Piqueras, Ernesto Nicolás, Ernest Giralt
2005 Journal of Computer-Aided Molecular Design  
We propose an evolutionary tool for de novo peptide design, based on the evaluation of energies for peptide binding to a user-defined protein surface patch.  ...  The software developed was successfully tested on the design of ligands for the proteins prolyl oligopeptidase, p53, and DNA gyrase.  ...  Traus for his creative input on the computational aspects of this work, and Prof. X. Vilasis for his mathematical support in the implementation of Bayesian network learning algorithms.  ... 
doi:10.1007/s10822-005-9015-1 pmid:16267689 fatcat:mbcfyecbpzc75gpwcfd566qmra

Computer-Aided Peptide Evolution for Virtual Drug Design [chapter]

Ignasi Belda, Xavier Llorà, Marc Martinell, Teresa Tarragó, Ernest Giralt
2004 Lecture Notes in Computer Science  
It provides an automatic tool for peptide de novo design, based on protein surface patches defined by user. A special emphasis has been given to the evaluation of the proposed peptides.  ...  Evolutionary computation provides a new approach to this design issue. A reliable framework for obtaining ligands via evolutionary algorithms has been implemented.  ...  The US Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation thereon.  ... 
doi:10.1007/978-3-540-24854-5_34 fatcat:liljnwsfxzaqjfalrkmittgkj4

Parallel multi-objective algorithms for the molecular docking problem [article]

Jean-Charles Boisson, Laetitia Jourdan, El-Ghazali Talbi
2008 arXiv   pre-print
We propose a new multi-objective model combining an energy term and a surface term to gain such complexes. The aim of our model is to provide complexes with a low energy and low surface.  ...  This model has been validated with two multi-objective genetic algorithms on instances from the literature dedicated to the docking benchmarking.  ...  Later, population based metaheuristics like Genetic Algorithms (GAs) have been used [2] , [3] . The current main algorithm included in AutoDock is based on a Lamarckian Genetic Algorithm (LGA).  ... 
arXiv:0811.0514v1 fatcat:whvlvyzgw5hfzcgko2a44bekli

Structure-based function prediction: approaches and applications

P. F. Gherardini, M. Helmer-Citterich
2008 Briefings in Functional Genomics & Proteomics  
Other methods try to identify functional patches on the surface of a protein using only its physicochemical characteristics.  ...  Existing methods can be roughly classified in two groups: some use a comparative approach looking for the presence of structural motifs possibly associated with a known biochemical function.  ...  Polacco and Babbitt [48] , for example, used a genetic algorithm to derive specific motifs that distinguish proteins belonging to a given enzymatic family from a background of unrelated structures.  ... 
doi:10.1093/bfgp/eln030 pmid:18599513 fatcat:brgwyqca3ffirfzl3bmvhrjvpi

Protein Structure Prediction as a Hard Optimization Problem: The Genetic Algorithm Approach

Mehul M. Khimasia, Peter V. Coveney
1997 Molecular Simulation  
The native conformations of proteins occupy a very small subset of these, hence an exploratory, robust search algorithm, such as a genetic algorithm (GA), is required.  ...  Furthermore, we introduce a statistical mechanical approach to analyse the genetic algorithm dynamics and suggest a convergence criterion using a quantity analogous to the free energy of a population.  ...  For this purpose we use a modified version of Goldberg's [24] Simple Genetic Algorithm (SGA), written in C.  ... 
doi:10.1080/08927029708024151 fatcat:oodstzimbveqtjolpgqgkbz57e
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