Filters








9,787 Hits in 7.0 sec

A NEW ALGORITHM FOR THE ALIGNMENT OF MULTIPLE PROTEIN STRUCTURES USING MONTE CARLO OPTIMIZATION

C. GUDA, E. D. SCHEEFF, P. E. BOURNE, I. N. SHINDYALOV
2000 Biocomputing 2001  
We have developed a new algorithm for the alignment of multiple protein structures based on a Monte Carlo optimization technique.  ...  The algorithm uses pair-wise structural alignments as a starting point. Four different types of moves were designed to generate random changes in the alignment.  ...  Here, we present a new algorithm for the alignment of multiple protein structures using Monte Carlo optimization method.  ... 
doi:10.1142/9789814447362_0028 fatcat:bcjd4752r5dsliqmqbmyk4b46u

CE-MC: a multiple protein structure alignment server

C. Guda, S. Lu, E. D. Scheeff, P. E. Bourne, I. N. Shindyalov
2004 Nucleic Acids Research  
CE-MC server (http://cemc.sdsc.edu) provides a webbased facility for the alignment of multiple protein structures based on C-a coordinate distances, using combinatorial extension (CE) and Monte Carlo (  ...  The whole process of generating multiple structure alignments involves three distinct steps, i.e. all-to-all pairwise alignment using the CE algorithm, iterative global optimization of a multiple alignment  ...  ACKNOWLEDGEMENTS The authors are grateful to Dr Kenji Mizuguchi for providing the JOY binaries and to Ms Jo-Lan Chung for her help with the user-friendliness of the server.  ... 
doi:10.1093/nar/gkh464 pmid:15215359 pmcid:PMC441602 fatcat:gw37ekoyvzfmlcgvcush7b455e

A Survey of Protein Fold Recognition Algorithms

Mohammed Said Abual-Rub, Rosni Abdullah
2008 Journal of Computer Science  
This problem is known as NPhard; researchers have used various methods such as neural networks, Monte Carlo, support vector machine and genetic algorithms to solve it.  ...  Problem statement: Predicting the tertiary structure of proteins from their linear sequence is really a big challenge in biology.  ...  Monte Carlo Evolutionary Monte Carlo for protein folding simulations [14] Evolutionary Monte Carlo approach for protein folding simulations A parallel hybrid GA for peptide 3-D structure prediction  ... 
doi:10.3844/jcssp.2008.768.776 fatcat:iqxcwkwe2jeibff4dntd7c6lmm

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 begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity.  ...  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

BioShell-Threading: versatile Monte Carlo package for protein 3D threading

Pawel Gniewek, Andrzej Kolinski, Andrzej Kloczkowski, Dominik Gront
2014 BMC Bioinformatics  
Our contribution presents a versatile tool for the fast and extensive aligning of two proteins with each other.  ...  The implemented Monte Carlo search engine greatly facilitates the development and benchmarking of new alignment scoring schemes even when the functions exhibit non-deterministic polynomial-time complexity  ...  The computational part of this work was done using the computer cluster at the Computing Center of the Department of Chemistry, University of Warsaw.  ... 
doi:10.1186/1471-2105-15-22 pmid:24444459 pmcid:PMC3937128 fatcat:i277kbm25nhcdiqgpp7d5xxfpe

Progressive combinatorial algorithm for multiple structural alignments: Application to distantly related proteins

María Elena Ochagavía, Shoshana Wodak
2004 Proteins: Structure, Function, and Bioinformatics  
MALECON is a progressive combinatorial procedure for multiple alignments of protein structures.  ...  The performance of MALECON is illustrated and compared with several extant multiple structure alignment methods by using as test the globin homologous superfamily, the OB and the Jellyrolls folds.  ...  Notredame for providing their structure alignments software for benchmarking and Jean Richelle for help with the computer systems.  ... 
doi:10.1002/prot.10587 pmid:15048834 fatcat:hekz5fd2cvasvdwsdm5p6yfhte

The Protein Folding Problem: A Biophysical Enigma

J. Fetrow, A. Giammona, A. Kolinski, J. Skolnick
2002 Current Pharmaceutical Biotechnology  
Protein folding technologies, while not yet providing a full understanding of the protein folding process, have clearly progressed to the point of being useful in enabling structure-based annotation of  ...  Although a complete understanding of the kinetics and thermodynamics of protein folding has remained elusive, there has been considerable progress in techniques to predict protein structure from amino  ...  preparation of the manuscript.  ... 
doi:10.2174/1389201023378120 pmid:12463416 fatcat:h7h7ovdjvvbfbg46zo3ekqi2da

Coupling the folding of homologous proteins

C. Keasar, D. Tobi, R. Elber, J. Skolnick
1998 Proceedings of the National Academy of Sciences of the United States of America  
The empirical observation that homologous proteins fold to similar structures is used to enhance the capabilities of an ab initio algorithm to predict protein conformations.  ...  Significant improvement in the quality of the computed structures (as compared with the computational folding of a single protein) is demonstrated and discussed.  ...  This research was supported by a Binational Science Foundation grant (to R.E. and J.S.) and by National Institutes of Health Grant GM37408 (to J.S.).  ... 
doi:10.1073/pnas.95.11.5880 pmid:9600887 pmcid:PMC34490 fatcat:rknkagwplbd3hevtmbyfnmzv7y

LAMBADA & InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations

Thomas H. Schmidt, Christian Kandt
2012 Biophysical Journal  
We show that LJ-PME has a significant effect on the surface tension and area per lipid of typical bilayers (up to 2% for DPPC, larger than differences targeted with new parameters), and present a new implementation  ...  This retains a well-defined Hamiltonian, and the effect is limited since the differences are smaller for large distances.  ...  The transmembrane potential and the ion concentrations were imposed by a Grand Canonical Monte-Carlo algorithm.  ... 
doi:10.1016/j.bpj.2011.11.938 fatcat:l26zaaa26bav7oxyh2oxuohwcy

Structure Comparison and Alignment [chapter]

Philip E. Bourne, Ilya N. Shindyalov
2005 Methods of biochemical analysis  
Davis for the Perl script to render LGL output graphs.  ...  MAMR and EC research is supported by the European Union (Marie Curie Program FP6-039722), the Spanish Ministerio de Educación y Ciencia (BIO2007/66670), and the Generalitat Valenciana (GV/2007/065).  ...  CE-MC (combinatorial extension-Monte Carlo) refines a set of pair-wise structure alignments using a Monte Carlo optimization technique.  ... 
doi:10.1002/0471721204.ch16 fatcat:rehizpnzsbbjfgi7jjef6slssm

Novel Metaheuristic-Based Approach for Solving Transmembrane Assembly using Limited Distance Information

Kanon Sujaree, Pornthep Sompornpisut
2012 Biophysical Journal  
We show that LJ-PME has a significant effect on the surface tension and area per lipid of typical bilayers (up to 2% for DPPC, larger than differences targeted with new parameters), and present a new implementation  ...  This retains a well-defined Hamiltonian, and the effect is limited since the differences are smaller for large distances.  ...  The transmembrane potential and the ion concentrations were imposed by a Grand Canonical Monte-Carlo algorithm.  ... 
doi:10.1016/j.bpj.2011.11.937 fatcat:imyyrzjhsvemtfrfqpjdmjuefy

Extended-System Adaptively Biased Simulations of Membrane Protein Orientation

Jérôme Hénin, Giacomo Fiorin
2012 Biophysical Journal  
We show that LJ-PME has a significant effect on the surface tension and area per lipid of typical bilayers (up to 2% for DPPC, larger than differences targeted with new parameters), and present a new implementation  ...  This retains a well-defined Hamiltonian, and the effect is limited since the differences are smaller for large distances.  ...  The transmembrane potential and the ion concentrations were imposed by a Grand Canonical Monte-Carlo algorithm.  ... 
doi:10.1016/j.bpj.2011.11.939 fatcat:rtel44kat5gyzovbag2k2zdnpy

Appendix [chapter]

Thomas Lengauer
2004 Bioinformatics - From Genomes to Drugs  
Acknowledgements I am grateful to Holger Clauûen, Daniel Homann, Jochen Selbig, Alexander Zien, and Ralf Zimmer for helpful comments on this glossary. Alexander Zien provided Figure 3 .  ...  . 3 Simulated annealing is a special instance of a Monte Carlo algorithm.  ...  In bioinformatics, clustering is used in the analysis of protein families ± sequence families and multiple alignment (Chapter 2 of Volume I), structure families (Chapter 6 of Volume I), or families of  ... 
doi:10.1002/3527601481.app1 fatcat:ihpjjubab5exnm4weky2ld2zde

Brownian Dynamics Simulation of Calcium Channels

Claudio Berti, Simone Furini, Dirk Gillespie, Dezsö Boda, Bob Eisenberg, Claudio Fiegna
2012 Biophysical Journal  
We show that LJ-PME has a significant effect on the surface tension and area per lipid of typical bilayers (up to 2% for DPPC, larger than differences targeted with new parameters), and present a new implementation  ...  This retains a well-defined Hamiltonian, and the effect is limited since the differences are smaller for large distances.  ...  The transmembrane potential and the ion concentrations were imposed by a Grand Canonical Monte-Carlo algorithm.  ... 
doi:10.1016/j.bpj.2011.11.940 fatcat:qgn6sftdjbfwvpm3kdvjyk3sfi

Proteins comparison through probabilistic optimal structure local alignment

Giovanni Micale, Alfredo Pulvirenti, Rosalba Giugno, Alfredo Ferro
2014 Frontiers in Genetics  
Here, we present PROPOSAL (PROteins comparison through Probabilistic Optimal Structure local ALignment), a stochastic algorithm based on iterative sampling for multiple local alignment of protein structures  ...  We also compared PROPOSAL with two state-of-the-art tools for pairwise local alignment on a dataset of manually annotated motifs.  ...  ACKNOWLEDGMENTS We wish to thank anonymous reviewer for their helpful suggestions and comments. We also wish to thank Dario Veneziano for reviewing the English of the final version of the article.  ... 
doi:10.3389/fgene.2014.00302 pmid:25228906 pmcid:PMC4151033 fatcat:rwnqsyjja5d3nmlab3rgmf7hhi
« Previous Showing results 1 — 15 out of 9,787 results