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Distance geometry optimization for protein structures. (English) Zbl 0944.92012

Summary: We study the performance of the dgsol code for the solution of distance geometry problems with lower and upper bounds on distance constraints. The dgsol code uses only a sparse set of distance constraints, while other algorithms tend to work with a dense set of constraints either by imposing additional bounds or by deducing bounds from the given bounds. Our computational results show that protein structures can be determined by solving a distance geometry problem with dgsol and that the approach based on dgsol is significantly more reliable and efficient than multi-starts with an optimization code.

MSC:

92C40 Biochemistry, molecular biology
51K99 Distance geometry
65K10 Numerical optimization and variational techniques
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