| Abstract
| - A new method for generating the low-energy structures of a chainmolecule was proposed recently by us.This is a stochastic process where at each step anenergy-minimized structure is changed by carrying outseveral local torsional deformations (LTDs) along the chain,which temporarily disrupt neighbors of the rotatedbonds. The energy is then minimized and the disrupted bonds returnto their usual geometry (in terms ofbond lengths and angles) while the chain assumes a new conformation.This conformation is accepted (andthen deformed) or rejected with the help of a “selection procedure”that gives preference to accepting thelower energy structures and, thus, directs the search toward the lowestenergy regions, which include theglobal energy minimum (GEM) structure. The selection procedurestested are the Monte Carlo minimization(MCM) method of Li and Scheraga and the “usage directed” (UD)method of Still's group. LTD is a generalmethod whose parameters can be optimized for any chain system.However, because of the local characterof the conformational change, it is expected to be especially efficientfor cyclic peptides, loops in proteins,and dense multichain systems. In this paper, LTD is applied tocycloheptadecane modeled by the MM2force field, its parameters are optimized, and it is found to be moreefficient than other methods. The resultsfor this molecule and for an ECEPP model of the linear pentapeptideLeu-enkephalin show that MCM andUD are almost comparable in efficiency, with a slight advantage forMCM.
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