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Combinatorial conformer problem

Conformational analysis is a combinatorial problem. The number of conformations for a molecule with n rotatable bonds is given by ... [Pg.195]

Virtual screening applications based on superposition or docking usually contain difficult-to-solve optimization problems with a mixed combinatorial and numerical flavor. The combinatorial aspect results from discrete models of conformational flexibility and molecular interactions. The numerical aspect results from describing the relative orientation of two objects, either two superimposed molecules or a ligand with respect to a protein in docking calculations. Problems of this kind are in most cases hard to solve optimally with reasonable compute resources. Sometimes, the combinatorial and the numerical part of such a problem can be separated and independently solved. For example, several virtual screening tools enumerate the conformational space of a molecule in order to address a major combinatorial part of the problem independently (see for example [199]). Alternatively, heuristic search techniques are used to tackle the problem as a whole. Some of them will be covered in this section. [Pg.85]

Combinatorial Distance Geometry Approach to the Calculation of Molecular Conformation. 1. A New Approach to an Old Problem. [Pg.49]

Because of the combinatorial nature of systematic search, one is often faced with large numbers of conformers that have to be analyzed. For some problems, energetic considerations are appropriate and conformers can be clustered with the closest local minimum, providing to a first approximation an estimate of the entropy associated with each minima by the number of conformers associated, in that they can come from a grid search that approximates the volume of the potential well. A single conformer, perhaps the one of lowest en-Qgy, can be used with appropriately adjusted error limits in further analyses as representative of the family. [Pg.93]

Side-chain conformation prediction is a combinatorial problem, since there are on the order of n ot possible conformations, where nrot is the average number of rotamers per side chain and N is the number of side chains. But in fact the space of conformations is much smaller than that, since side chains can only interact with a small number of neighbors, and in most cases clusters of interacting side chains can be isolated and each cluster can be solved separately [93, 165]. Also, many rotamers have prohibitively large interactions with the backbone and are at the outset unlikely to be part of the final predicted conformation. These can be eliminated from the search early on. [Pg.197]

T. F. Havel, I. D. Kuntz, and G. M. Crippen. The combinatorial distance geometry approach to the calculation of molecular conformation I. a new approach to an old problem. Journal of Theoretical Biology, 104 359-381, 1983. [Pg.366]

Systematic grid searches represent a combinatorial problem and this is a major drawback of this technique. The number of possible conformations N... [Pg.182]

Another way to simplify the tertiary structure problem is to fix the backbone and then carry out an exhaustive search on the allowed side chain conformations. Desmet and co-workers have developed a dead-end elimination method for searching side chain conformations. Side chain conformations are grouped into a limited set of allowed rotamers. While an exhaustive search of all possible combinations of these rotamers is still not feasible, the application of the dead-end elimination theorem allows removal of impossible combinations early in the search, thus controlling the combinatorial explosion and leading to a small group of possible final solutions. The possible solutions can then be compared to find the best possible structure. [Pg.353]


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Combinatorial problem

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