RAMBLE: a conformational search program.
A program, RAMBLE, is described which searches the conformational space of looped or cyclic molecules by random assignment of internal coordinates. Conformations produced are screened for energetically unfavorable intramolecular contacts and are subject to user-supplied constraints in terms of both bonded and nonbonded distances, bond angles, and torsion angles. The methodology employed is discussed in relation to alternative search strategies, and a description is given of its successful application in modeling the structures of cyclohexane, reverse-turn tetrapeptides, and a bacterial siderophore complex.
Cluster Analysis↗