Literature DB >> 14525223

Unbiased global optimization of Lennard-Jones clusters for N < or =201 using the conformational space annealing method.

Julian Lee1, In-Ho Lee, Jooyoung Lee.   

Abstract

We apply the conformational space annealing method to the Lennard-Jones clusters and find all known lowest energy configurations up to 201 atoms, without using extra information of the problem such as the structures of the known global energy minima. In addition, the robustness of the algorithm with respect to the randomness of initial conditions of the problem is demonstrated by ten successful independent runs up to 183 atoms. Our results indicate that this method is a general and yet efficient global optimization algorithm applicable to many systems.

Entities:  

Year:  2003        PMID: 14525223     DOI: 10.1103/PhysRevLett.91.080201

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  12 in total

1.  Architecture of the type IV coupling protein complex of Legionella pneumophila.

Authors:  Mi-Jeong Kwak; J Dongun Kim; Hyunmin Kim; Cheolhee Kim; James W Bowman; Seonghoon Kim; Keehyoung Joo; Jooyoung Lee; Kyeong Sik Jin; Yeon-Gil Kim; Nam Ki Lee; Jae U Jung; Byung-Ha Oh
Journal:  Nat Microbiol       Date:  2017-07-17       Impact factor: 17.745

2.  Multiple sequence alignment by conformational space annealing.

Authors:  Keehyoung Joo; Jinwoo Lee; Ilsoo Kim; Sung Jong Lee; Jooyoung Lee
Journal:  Biophys J       Date:  2008-08-08       Impact factor: 4.033

3.  Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.

Authors:  Elmar Krieger; Keehyoung Joo; Jinwoo Lee; Jooyoung Lee; Srivatsan Raman; James Thompson; Mike Tyka; David Baker; Kevin Karplus
Journal:  Proteins       Date:  2009

4.  Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Authors:  Juyong Lee; Florentina Tofoleanu; Frank C Pickard; Gerhard König; Jing Huang; Ana Damjanović; Minkyung Baek; Chaok Seok; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

5.  Improved network community structure improves function prediction.

Authors:  Juyong Lee; Steven P Gross; Jooyoung Lee
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

6.  Finding multiple reaction pathways via global optimization of action.

Authors:  Juyong Lee; In-Ho Lee; InSuk Joung; Jooyoung Lee; Bernard R Brooks
Journal:  Nat Commun       Date:  2017-05-26       Impact factor: 14.919

7.  Non-sequential protein structure alignment by conformational space annealing and local refinement.

Authors:  InSuk Joung; Jong Yun Kim; Keehyoung Joo; Jooyoung Lee
Journal:  PLoS One       Date:  2019-01-30       Impact factor: 3.240

8.  Hidden information revealed by optimal community structure from a protein-complex bipartite network improves protein function prediction.

Authors:  Juyong Lee; Jooyoung Lee
Journal:  PLoS One       Date:  2013-04-05       Impact factor: 3.240

9.  Dipole-allowed direct band gap silicon superlattices.

Authors:  Young Jun Oh; In-Ho Lee; Sunghyun Kim; Jooyoung Lee; Kee Joo Chang
Journal:  Sci Rep       Date:  2015-12-11       Impact factor: 4.379

10.  Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise.

Authors:  Juyong Lee; Zhong-Yuan Zhang; Jooyoung Lee; Bernard R Brooks; Yong-Yeol Ahn
Journal:  Sci Rep       Date:  2017-09-29       Impact factor: 4.379

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