The hierarchical organization of molecular structure computations

The task of computing molecular structure from combinations of experimental and theoretical constraints is expensive because of the large number of estimated parameters (the 3D coordinates of each atom) and the rugged landscape of many objective functions. For large molecular ensembles with multiple protein and nucleic acid components, the problem of maintaining tractability in structural computations becomes critical. A well known strategy for solving difficult problems is divide and conquer. For molecular computations, there are two ways in which problems can be divided: (1) using the natural hierarchy within biological macromolecules (taking advantage of primary sequence, secondary structural subunits and tertiary structural motifs, when they are known), and (2) using the hierarchy that results from analyzing the distribution of structural constraints (providing information about which substructures are constrained to one another). In this paper, we show that these two hierarchies ...

• Type: Conference
• Year: 1998
• Where: RECOMB
• Authors: Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman
• Keywords: Computational Biology, Empirical Hierarchies, Natural Hierarchy, RECOMB 1998, Structural Computations