Parallel continuation-based global optimization for molecular conformation and protein folding
- Cornell Univ., Ithaca, NY (United States)
This paper presents the authors` recent work on developing parallel algorithms and software for solving the global minimization problem for molecular conformation, especially protein folding. Global minimization problems are difficult to solve when the objective functions have many local minimizers, such as the energy functions for protein folding. In their approach, to avoid directly minimizing a ``difficult`` function, a special integral transformation is introduced to transform the function into a class of gradually deformed, but ``smoother`` or ``easier`` functions. An optimization procedure is then applied to the new functions successively, to trace their solutions back to the original function. The method can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation and protein folding. Mathematical theory for the method, as a special continuation approach to global optimization, is established. Algorithms with different solution tracing strategies are developed. Different levels of parallelism are exploited for the implementation of the algorithms on massively parallel architectures.
- Research Organization:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Organization:
- Cornell Univ., Ithaca, NY (United States); National Science Foundation, Washington, DC (United States); Department of Defense, Washington, DC (United States); National Insts. of Health, Bethesda, MD (United States); New York State Government, Albany, NY (United States)
- DOE Contract Number:
- W-31109-ENG-38
- OSTI ID:
- 34354
- Report Number(s):
- ANL/MCS/CP-83621; CONF-941118-10; ON: DE95005860; TRN: AHC29511%%64
- Resource Relation:
- Conference: Supercomputing `94 meeting, Washington, DC (United States), 14-18 Nov 1994; Other Information: PBD: [1994]
- Country of Publication:
- United States
- Language:
- English
Similar Records
A parallel global optimization method for solving molecular cluster and polymer conformation problems
Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure