A parallel hybrid genetic algorithm for protein structure prediction on the computational grid

[1]  B. Alder,et al.  Phase Transition for a Hard Sphere System , 1957 .

[2]  B. Alder,et al.  Studies in Molecular Dynamics. I. General Method , 1959 .

[3]  C. Levinthal How to fold graciously , 1969 .

[4]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[5]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[6]  Jared L. Cohon,et al.  6 – Multicriteria programming: brief review and application , 1985 .

[7]  J T Ngo,et al.  Computational complexity of a problem in molecular structure prediction. , 1992, Protein engineering.

[8]  H A Scheraga,et al.  Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator , 1996, Protein science : a publication of the Protein Society.

[9]  Miron Livny,et al.  Mechanisms for High Throughput Computing , 1997 .

[10]  Arnold Neumaier,et al.  Molecular Modeling of Proteins and Mathematical Prediction of Protein Structure , 1997, SIAM Rev..

[11]  G. Grassy,et al.  Glossary of terms used in computational drug design (IUPAC Recommendations 1997) , 1997 .

[12]  Mihalis Yannakakis,et al.  On the Complexity of Protein Folding , 1998, J. Comput. Biol..

[13]  R. Nussinov,et al.  Folding funnels and binding mechanisms. , 1999, Protein engineering.

[14]  William E. Hart,et al.  Protein structure prediction with evolutionary algorithms , 1999 .

[15]  Johannes Grotendorst,et al.  Modern methods and algorithms of quantum chemistry , 2000 .

[16]  H. Dorsett,et al.  Overview of Molecular Modelling and Ab initio Molecular Orbital Methods Suitable for Use with Energetic Materials , 2000 .

[17]  F. Zerilli,et al.  Ab Initio Calculation of Intermolecular Potential Parameters for Gaseous Decomposition Products of Energetic Materials , 2000 .

[18]  Jeff T. Linderoth,et al.  An enabling framework for master-worker applications on the Computational Grid , 2000, Proceedings the Ninth International Symposium on High-Performance Distributed Computing.

[19]  Richard Bonneau,et al.  Rosetta in CASP4: Progress in ab initio protein structure prediction , 2001, Proteins.

[20]  Richard A. Watson,et al.  Reducing Local Optima in Single-Objective Problems by Multi-objectivization , 2001, EMO.

[21]  Eaton E. Lattman CASP4 , 2001 .

[22]  Subhash Saini,et al.  Scalable atomistic simulation algorithms for materials research , 2001, SC.

[23]  El-Ghazali Talbi,et al.  A Taxonomy of Hybrid Metaheuristics , 2002, J. Heuristics.

[24]  Subhash Saini,et al.  Scalable atomistic simulation algorithms for materials research , 2002 .

[25]  Subhash Saini,et al.  Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan , 2002, ACM/IEEE SC 2002 Conference (SC'02).

[26]  Thom Vreven,et al.  Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints , 2003, J. Comput. Chem..

[27]  Brian E. Moore,et al.  Multi-symplectic integration methods for Hamiltonian PDEs , 2003, Future Gener. Comput. Syst..

[28]  Pierre-Yves Calland On the structural complexity of a protein. , 2003, Protein engineering.

[29]  Alvaro L. Islas,et al.  Multi-symplectic methods for generalized Schrödinger equations , 2003, Future Gener. Comput. Syst..

[30]  Francine Berman,et al.  Grid Computing: Making the Global Infrastructure a Reality , 2003 .

[31]  El-Ghazali Talbi,et al.  ParadisEO: A Framework for the Reusable Design of Parallel and Distributed Metaheuristics , 2004, J. Heuristics.

[32]  Internal friction in the ultrafast folding of the tryptophan cage , 2004 .

[33]  Linlin Qiu,et al.  Internal friction in the ultrafast folding of the tryptophan cage , 2004 .

[34]  Douglas Thain,et al.  Distributed computing in practice: the Condor experience , 2005, Concurr. Pract. Exp..

[35]  Enrique Alba,et al.  Metaheuristics and Parallelism , 2005 .

[36]  El-Ghazali Talbi,et al.  An enabling framework for parallel optimization on the computational grid , 2005, CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005..

[37]  Benjamin Parent,et al.  Optimized Evolutionary Strategies in Conformational Sampling , 2006, Soft Comput..

[38]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[39]  Journal of Chemical Physics , 1932, Nature.