For conformational searching

Method and a Genetic Algorithm for Conformational Searching. Journal of Computational... 

The choice of heating time depends on the purpose of the molecular dynamics simulation. If the simulation is for conformational searches, the heating step is not critical for a successful calculation. The heating step may be rapid to induce large structural changes that provide access to more of the conformational space. 

R Abagyan, P Argos. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. I Mol Biol 225 519-532, 1992. 

Hudson, B. D., George, A. R., Ford, M. G., and Livingstone, D. J. (1992) Structure-activity relation ships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation.. /. Comput-Aided Mol. Design 6, 191-201. 

Molecular mechanics calculations do not show up on the chart. They are at least an order of magnitude less costly than the simplest (semi-empirical) quantum chemical calculations, and the ratio between the two increases rapidly with increasing molecular size. Molecular mechanics is really the only viable alternative at present for molecules comprising more than a few hundred atoms. It is also likely to be the only practical alternative for conformational searching on molecules with more than a few degrees of freedom. 

Molecular mechanics models are restricted to the description of molecular equilibrium geometry and conformation. They are the method of choice for conformational searching on complex systems. 

Transition metal (TM) systems present a fundamental dilemma for computational chemists. On the one hand, TM centers are often associated with relatively complicated electronic structures which appear to demand some form of quantum mechanical (QM) approach (1). On the other hand, all forms of QM are relatively compute intensive and are impractical for conformational searching, virtual high-throughput screening, or dynamics simulations... 

Saunders M, Houk KN, Wu YD, Still WC, Lipton M, Chang G, Guida WC. Conformations of cycloheptadecane. A comparison of methods for conformational searching. J Am Chem Soc 1990 112 1419-1427. 

Tertiary Conformation of Marine Snail a-Conotoxin Strategy for Conformational Searching Using Molecular Dynamics. ... 

We extended the use of our program Anneal-Conformer and the Amber force field for conformation searching of peptides [5]. We were also able to efficiently locate several new families of active conformations of Met-enkephalin [6]. Similar studies of Met-enkephalin Kawai [7] on a simplified ECEPP energy surface also demonstrated the efficiency of simulated annealing. 

MMFF94 A tool for conformational searching of highly flexible molecules... 

A. E. Howard and P. A. Kollman, ]. Med. Chem., 31, 1675 (1988). An Analysis of Current Methodologies for Conformational Searching of Complex Molecules. A. R. Leach, this volume. A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. 

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