Literature DB >> 10464088

Global optimization of clusters, crystals, and biomolecules.

D J Wales1, H A Scheraga.   

Abstract

Finding the optimal solution to a complex optimization problem is of great importance in many fields, ranging from protein structure prediction to the design of microprocessor circuitry. Some recent progress in finding the global minima of potential energy functions is described, focusing on applications of the simple "basin-hopping" approach to atomic and molecular clusters and more complicated hypersurface deformation techniques for crystals and biomolecules. These methods have produced promising results and should enable larger and more complex systems to be treated in the future.

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Year:  1999        PMID: 10464088     DOI: 10.1126/science.285.5432.1368

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  62 in total

1.  Investigation of routes and funnels in protein folding by free energy functional methods.

Authors:  S S Plotkin; J N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2000-06-06       Impact factor: 11.205

2.  A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins.

Authors:  Meir Glick; Anwar Rayan; Amiram Goldblum
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-15       Impact factor: 11.205

3.  Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.

Authors:  Zhexin Xiang; Cinque S Soto; Barry Honig
Journal:  Proc Natl Acad Sci U S A       Date:  2002-05-28       Impact factor: 11.205

4.  Modeling and design by hierarchical natural moves.

Authors:  Adelene Y L Sim; Michael Levitt; Peter Minary
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-23       Impact factor: 11.205

5.  Protein folded states are kinetic hubs.

Authors:  Gregory R Bowman; Vijay S Pande
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-01       Impact factor: 11.205

6.  Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm.

Authors:  Peter Minary; Michael Levitt
Journal:  J Comput Biol       Date:  2010-08       Impact factor: 1.479

7.  Conformational study of Met-enkephalin based on the ECEPP force fields.

Authors:  Lixin Zhan; Jeff Z Y Chen; Wing-Ki Liu
Journal:  Biophys J       Date:  2006-07-07       Impact factor: 4.033

8.  Improved evolutionary optimization from genetically adaptive multimethod search.

Authors:  Jasper A Vrugt; Bruce A Robinson
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

9.  Destruction of long-range interactions by a single mutation in lysozyme.

Authors:  Ruhong Zhou; Maria Eleftheriou; Ajay K Royyuru; Bruce J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-26       Impact factor: 11.205

10.  Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.

Authors:  Keren Lasker; Maya Topf; Andrej Sali; Haim J Wolfson
Journal:  J Mol Biol       Date:  2009-02-20       Impact factor: 5.469

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