title: Global energy minimization of alanine dipeptide via barrier function methods.
abstract: This paper presents an interior point method to determine the minimum energy conformation of alanine dipeptide. The CHARMM energy function is minimized over the internal coordinates of the atoms involved. A barrier function algorithm to determine the minimum energy conformation of peptides is proposed. Lennard-Jones 6-12 potential which is used to model the van der Waals interactions in the CHARMM energy equation is used as the barrier function for this algorithm. The results of applying the algorithm for the alanine dipeptide structure as a function of varying number of dihedral angles are reported, and they are compared with that obtained from genetic algorithm approach. In addition, the results for polyalanine structures are also reported.
authors.affiliation: Department of Industrial and Systems Engineering, National University of Singapore, Singapore. isenkm@nus.edu.sg
authors.forename: Kien Ming
authors.initials: KM
authors.lastname: Ng
authors.forename: Muthu
authors.initials: M
authors.lastname: Solayappan
authors.forename: Kim Leng
authors.initials: KL
authors.lastname: Poh
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D004151:Dipeptides; D000409:Alanine