Search Medium-sized Molecules

Boyd and P. J. Philips, The Science of Polymer Molecules, Cambridge University Press, Cambridge, 1993. 

Albinsson, D. Antic, F. Neumann, and J. Michl, unpublished results. 

Another point to note with this algorithm is that each perturbation given to the molecule is local and weak, so that the new conformations produced are supposed to lie close to the starting conformer. This aspect produces a distinctive advantage, as will be shown below. 

When a starting conformer is somehow chosen and given one round of small perturbations to all the movable portions of the molecule, several new conformers are generally obtained, and they are more or less similar in structure and energy to the starting conformer. Then the most stable of the new conformers is selected for the next starting point and the perturbation/geometry optimization routine is repeated until 

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Conformational Sampling Conformational Search Linear Chains Conformational Search Medium-sized Molecules Systematic and Random Search Methods for Finding Conformers of Molecules. 

Many of the techniques described previously for structure prediction of macromolecules and docking predictions can be applied to the conformation analysis of small molecules with a view to energy minimization or constraint satisfaction. (See Conformational Analysis 1 Conformational Analysis 2 Conformational Analysis 3 Conformational Search Linear Chains Conformational Search Medium-sized Molecules and Conformational Search Proteins.)... 

Comparative Molecular Field Analysis (CoMFA) Conformational Flexibility in 3D Structure Searching Conformational Search Medium-sized Molecules Conformational Search Proteins Genetic and Evolutionary Algorithms Molecular Docking and Structure-based Design Shape Analysis Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases. 

Conformational Search Medium-sized Molecules Dopamine Agonists, Antagonists, and Reuptake Blockers Drug... 

Molecular dynamics simulations are el ficient for searching the conformational space of medium-sized molecules and peptides. Different protocols can increase the elTicieiicy of the search and reduce the computer time needed to sample adequately the available conformations. 

The most serious problem with MM as a method to predict molecular structure is convergence to a false, rather than the global minimum in the Born-Oppenheimer surface. The mathematical problem is essentially still unsolved, but several conformational searching methods for approaching the global minimum, and based on either systematic or random searches have been developed. These searches work well for small to medium-sized molecules. The most popular of these techniques that simulates excitation to surmount potential barriers, has become known as Molecular Dynamics [112]. 

Andrew R. Leach, A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. 

Leach, A.R.(1991)A survey of methods for searching the conformational space of small and medium-sized molecules. In Reviews in computational chemistry, Lipkowitz, K. B. and Boyd, D. B. (eds.), VCH Publishers, New York, Vol. 2, pp. 1-55. 

A. R. Leach, in Reviews in Computational Chemistry, Vol. 2, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1991. A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. 

Several commercially available program packages such as SPARTAN or the Cerius2 system include routines or modules to systematically search the conformational space of small-sized and medium-sized molecules [38,39]. Additionally, some methods offer the possibility to generate the conformations under geometrical constraints to output only those structures that, for example, fulfill a given pharmacophore model within a certain range. 

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