scholarly journals Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

RNA ◽  
2004 ◽  
Vol 10 (8) ◽  
pp. 1178-1190 ◽  
Author(s):  
D. H. MATHEWS
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Partition Function ◽  
Energy Minimization ◽  
Rna Secondary Structure ◽  
Base Pairs ◽  
Free Energy Minimization

scholarly journals An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots

BMC Genomics ◽  
2019 ◽  
Vol 20 (S13) ◽  
Author(s):  
Zhang Kai ◽  
Wang Yuting ◽  
Lv Yulin ◽  
Liu Jun ◽  
He Juanjuan
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Simulated Annealing Algorithm ◽  
Secondary Structure Prediction ◽  
Stem Length ◽  
Base Pairs ◽  
Rna Secondary Structure Prediction ◽  
Prediction Algorithms

Abstract Background RNA pseudoknot structures play an important role in biological processes. However, existing RNA secondary structure prediction algorithms cannot predict the pseudoknot structure efficiently. Although random matching can improve the number of base pairs, these non-consecutive base pairs cannot make contributions to reduce the free energy. Result In order to improve the efficiency of searching procedure, our algorithm take consecutive base pairs as the basic components. Firstly, our algorithm calculates and archive all the consecutive base pairs in triplet data structure, if the number of consecutive base pairs is greater than given minimum stem length. Secondly, the annealing schedule is adapted to select the optimal solution that has minimum free energy. Finally, the proposed algorithm is evaluated with the real instances in PseudoBase. Conclusion The experimental results have been demonstrated to provide a competitive and oftentimes better performance when compared against some chosen state-of-the-art RNA structure prediction algorithms.

Comments on the Antonow and interfacial interaction rules

1990 ◽  
Vol 55 (5) ◽  
pp. 1143-1148 ◽  
Author(s):  
Jan Kloubek
Keyword(s):  
Free Energy ◽  
Energy Minimization ◽  
Interfacial Interaction ◽  
Aliphatic Hydrocarbon ◽  
Theoretical Base ◽  
Water Interface ◽  
Free Energy Minimization ◽  
Interaction Rule

Results presented for the aliphatic hydrocarbon-water interface show that the recent hypothesis of the free energy minimization called interfacial interaction rule, which was suggested as a theoretical base of the Antonow rule, cannot be generally valid.

scholarly journals Linking RNA Secondary Structure to the Free Energy of Tertiary Structure Folding through Coarse-Grained Models

2014 ◽  
Vol 106 (2) ◽  
pp. 284a
Author(s):  
Anthony M. Mustoe ◽  
Hashim M. Al-Hashimi ◽  
Charles L. Brooks
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Tertiary Structure ◽  
Coarse Grained

scholarly journals Entropy maximization and free energy minimization of multiphase mixtures using particle swarm optimization

2018 ◽  
Author(s):  
Philip C. Myint ◽  
Brian T. Gersten ◽  
Matthew A. McClelland ◽  
Albert L. Nichols ◽  
H. Keo Springer
Keyword(s):  
Free Energy ◽  
Particle Swarm Optimization ◽  
Energy Minimization ◽  
Particle Swarm ◽  
Swarm Optimization ◽  
Entropy Maximization ◽  
Free Energy Minimization

scholarly journals Free-energy minimization in joint agent-environment systems: A niche construction perspective

2018 ◽  
Vol 455 ◽  
pp. 161-178 ◽  
Author(s):  
Jelle Bruineberg ◽  
Erik Rietveld ◽  
Thomas Parr ◽  
Leendert van Maanen ◽  
Karl J Friston
Keyword(s):  
Free Energy ◽  
Energy Minimization ◽  
Niche Construction ◽  
Free Energy Minimization
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