An improved energy landscape paving algorithm for the problem of packing circles into a larger containing circle

2009 ◽  
Vol 57 (3) ◽  
pp. 1144-1149 ◽  
Author(s):  
Jingfa Liu ◽  
Shengjun Xue ◽  
Zhaoxia Liu ◽  
Danhua Xu
Keyword(s):  
Energy Landscape ◽  
Energy Landscape Paving

Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins

2013 ◽  
Vol 88 (5) ◽  
Author(s):  
Jingfa Liu ◽  
Beibei Song ◽  
Zhaoxia Liu ◽  
Weibo Huang ◽  
Yuanyuan Sun ◽  
...  
Keyword(s):  
Lattice Model ◽  
Energy Landscape ◽  
Face Centered Cubic ◽  
Face Centered ◽  
Energy Landscape Paving

STUDIES OF FINDING LOW ENERGY CONFIGURATIONS IN OFF-LATTICE PROTEIN MODELS

2006 ◽  
Vol 05 (03) ◽  
pp. 587-594 ◽  
Author(s):  
JINGFA LIU ◽  
WENQI HUANG
Keyword(s):  
Lower Energy ◽  
Gradient Descent ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Ground States ◽  
Low Energy ◽  
Protein Models ◽  
Energy Configurations ◽  
Energy Landscape Paving ◽  
Lattice Protein Models

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

Energy landscape paving simulations of the trp-cage protein

2005 ◽  
Vol 122 (19) ◽  
pp. 194711 ◽  
Author(s):  
Alexander Schug ◽  
Wolfgang Wenzel ◽  
Ulrich H. E. Hansmann
Keyword(s):  
Energy Landscape ◽  
Energy Landscape Paving

Energy landscape paving with local search for global optimization of the BLN off-lattice model

2014 ◽  
Vol 64 (4) ◽  
pp. 603-610 ◽  
Author(s):  
Jingfa Liu ◽  
Weibo Huang ◽  
Wenjie Liu ◽  
Beibei Song ◽  
Yuanyuan Sun ◽  
...  
Keyword(s):  
Global Optimization ◽  
Local Search ◽  
Lattice Model ◽  
Energy Landscape ◽  
Energy Landscape Paving

A FAST AND EFFECTIVE CONFORMATIONAL SEARCH METHOD FOR PEPTIDES

2003 ◽  
Vol 14 (07) ◽  
pp. 985-991 ◽  
Author(s):  
HANDAN ARKIN ◽  
TARIK ÇELIK
Keyword(s):  
Monte Carlo ◽  
Hybrid Algorithm ◽  
Energy Landscape ◽  
Search Method ◽  
Low Energy ◽  
Conformational Search ◽  
Energy Landscape Paving ◽  
Low Energy Conformations

We propose a hybrid algorithm, which combines the features of the energy landscape paving (ELP) and Monte Carlo Minimization (MCM) methods. We have tested its performance in studying the low-energy conformations of the heptapeptide deltorphin.

A COMBINATION OF REPLICA EXCHANGE MONTE CARLO AND ENERGY LANDSCAPE PAVING ALGORITHMS TO INCREASE THE EFFECTIVENESS OF CONFORMATIONAL SAMPLING

2004 ◽  
Vol 15 (07) ◽  
pp. 933-937 ◽  
Author(s):  
HANDAN ARKIN
Keyword(s):  
Monte Carlo ◽  
Hybrid Algorithm ◽  
Energy Landscape ◽  
Monte Carlo Sampling ◽  
Replica Exchange ◽  
Conformational Sampling ◽  
Sampling Techniques ◽  
Replica Exchange Monte Carlo ◽  
Energy Landscape Paving ◽  
Low Energy Conformations

A combination of replica exchange Monte Carlo sampling techniques and energy landscape paving approach is presented. This hybrid algorithm combines the features of the energy landscape paving (ELP) and replica exchange methods (REM). I have tested its performance in studying the low-energy conformations of the benchmark peptide Met-enkephalin.

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