, Volume 2, Issue 3, pp 319-331

Rigid versus unique determination of protein structures with geometric buildup

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Abstract

We introduce a geometric buildup approach to the distance geometry problem in protein modeling, and discuss the necessary and sufficient conditions on the distances for rigid or unique determination of a protein structure. We describe a new buildup algorithm for determining protein structures rigidly instead of uniquely. The algorithm requires even fewer distance constraints than the general buildup algorithm. We present the test results from applying the algorithm to determining the protein structures with varying degrees of availability of the distances, and show that the new development increases the modeling ability of the geometric buildup method even more while retaining much of the computational feasibility of the method.