Practical methods of optimization; (2nd ed.)
Practical methods of optimization; (2nd ed.)
Computer simulation of liquids
Computer simulation of liquids
A fast recursive algorithm for molecular dynamics simulation
Journal of Computational Physics
Distance Geometry Optimization for Protein Structures
Journal of Global Optimization
Ab initio Tertiary Structure Prediction of Proteins
Journal of Global Optimization
Deterministic Global Optimization: Theory, Methods and (NONCONVEX OPTIMIZATION AND ITS APPLICATIONS Volume 37) (Nonconvex Optimization and Its Applications)
Research Article: Global energy minimization of alanine dipeptide via barrier function methods
Computational Biology and Chemistry
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First principles approaches to the protein structure prediction problem must search through an enormous conformational space to identify low-energy, near-native structures. In this paper, we describe the formulation of the tertiary structure prediction problem as a nonlinear constrained minimization problem, where the goal is to minimize the energy of a protein conformation subject to constraints on torsion angles and interatomic distances. The core of the proposed algorithm is a hybrid global optimization method that combines the benefits of the 驴BB deterministic global optimization approach with conformational space annealing. These global optimization techniques employ a local minimization strategy that combines torsion angle dynamics and rotamer optimization to identify and improve the selection of initial conformations and then applies a sequential quadratic programming approach to further minimize the energy of the protein conformations subject to constraints. The proposed algorithm demonstrates the ability to identify both lower energy protein structures, as well as larger ensembles of low-energy conformations.