Cartesian random search

Dmparison of various methods for searching conformational space has been performed cycloheptadecane (C17H34) [Saunders et al. 1990]. The methods compared were the ematic search, random search (both Cartesian and torsional), distance geometry and ecular dynamics. The number of unique minimum energy conformations found with 1 method within 3 kcal/mol of the global minimum after 30 days of computer processing e determined (the study was performed in 1990 on what would now be considered a / slow computer). The results are shown in Table 9.1. 

SCAMPI reads multiple MOL2 files containing structures and a data file containing the biological activities. The conformational expansion of the molecules is done by applying random search techniques, with no post-clustering. This search is performed in Cartesian and internal coordinate space. 

Cartesian and Internal Coordinate Random Search Methods... 

The Cartesian and dihedral versions of the random search differ in the way in which each new structure is generated. The Cartesian method adds a random amount to the x, y and z coordinates of all the atoms in the molecule [Saunders 1987 Ferguson and Raber 1989]... 

Conformational isomers represent minima on an energy surface, and all structures and the corresponding strain energies can be obtained by a careful analysis. This can be performed manually (such as in Sections 17.3 and 17.4) or automatically. An automatic procedure may involve a systematic search (grid search methods), a stochastic search (e.g., torsional Monte Carlo or cartesian stochastic, i.e., the random kick method) or molecular dynamics (see Chapter 5 and Section 16.5). Implemented in MOMEC is a random kick stochastic search module, and this has been shown to lead to excellent results, not only for conformational equilibria, but also for distributions of configurational isomers[37]. 

Ferguson and Raber s RIPS (Random Incremental Pulse Search) program also performs its stochastic search in Cartesian coordinate space. Two modes of operation are possible, the first to locate just the global minimum energy conformation and the second to perform a complete search of the conformational space. In the hunt for the global energy minimum, the lowest energy structure found to... 

Saunders 26 introduced a method that performs random molecular conformational searches in Cartesian rather than internal space. In this method, one starts with an initial conformation. Every atom in the molecule is given a... 

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