A fast recursive algorithm for molecular dynamics simulation
Journal of Computational Physics
Prediction of Oligopeptide Conformations via Deterministic Global Optimization
Journal of Global Optimization
Deterministic Global Optimization: Theory, Methods and (NONCONVEX OPTIMIZATION AND ITS APPLICATIONS Volume 37) (Nonconvex Optimization and Its Applications)
Enhanced bounding techniques to reduce the protein conformational search space
Optimization Methods & Software - GLOBAL OPTIMIZATION
A review of recent advances in global optimization
Journal of Global Optimization
Journal of Global Optimization
Scatter Search algorithm for Protein Structure Prediction
International Journal of Bioinformatics Research and Applications
An improved hybrid global optimization method for protein tertiary structure prediction
Computational Optimization and Applications
A network flow model for biclustering via optimal re-ordering of data matrices
Journal of Global Optimization
Journal of Global Optimization
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A daunting challenge in the area of computational biology has been to develop a method to theoretically predict the correct three-dimensional structure of a protein given its linear amino acid sequence. The ability to surmount this challenge, which is known as the protein folding problem, has tremendous implications. We introduce a novel ab initio approach for the protein folding problem. The accurate prediction of the three-dimensional structure of a protein relies on both the mathematical model used to mimic the protein system and the technique used to identify the correct structure. The models employed are based solely on first principles, as opposed to the myriad of techniques relying on information from statistical databases. The framework integrates our recently proposed methods for the prediction of secondary structural features including helices and strands, as well as β-sheet and disulfide bridge formation. The final stage of the approach, which culminates in the tertiary structure prediction of a protein, utilizes search techniques grounded on the foundations of deterministic global optimization, powerful methods which can potentially guarantee the correct identification of a protein's structure. The performance of the approach is illustrated with bovine pancreatic trypsin inhibitor protein and the immunoglobulin binding domain of protein G.