Optimization in Computational Chemistry and Molecular Biology

Preface. Predicting Protein Tertiary Structure using a Global Optimization Algorithm with Smoothing; A. Azmi, et al. Methodology for Elucidating the Folding Dynamics of Peptides: Met-enkephalin Case Study; J.L. Klepeis, C.A. Floudas. Energy Landscape Projections of Molecular Potential Functions; A.T. Phillips, et al. Global Optimization and Sampling in the Context of Tertiary Structure Prediction: A Comparison of Two Algorithms; V.A. Eyrich, et al. Protein Folding Simulations by Monte Carlo Simulated Annealing and Multicanonical Algorithm; Y. Okamoto. Thermodynamics of Protein Folding - The Generalized-Ensemble Approach; U.H.E. Hansmann. An approach to detect the dominant folds of proteinlike heteropolymers from the statistics of a homopolymeric chain; E.D. Nelson, et al. Gene Sequences are Locally Optimized for Global mRNA Folding; W. Seffens, D. Digby. Structure Calculations of Symmetric Dimers using Molecular Dynamics/Simulated Annealing and NMR Restraints: The Case of the RIIalpha Subunit of Protein Kinase A; D. Morikis, et al. Structure Prediction of Binding States of MHC Class II Molecules based on the Crystal of HLA-DRB1 and Global Optimization; M.G. Ierapetritou, et al. A Coupled Scanning and Optimization Scheme for Analyzing Molecular Interactions; J.C. Mitchell, et al. Improved Evolutionary Hybrids for Flexible Ligand Docking in AutoDock; W.E. Hart, et al. Electrostatic Optimization in Ligand Complementarity and Design; E. Kangas, B. Tidor. Exploring potential solvation sites of proteins by multistart local minimization; S. Dennis, et al. On relative position of two biopolymer molecules minimizing the weighted sum of interatomic distances squared; A.B. Bogatyrev. Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization; D. Xie, T. Schlick. Optimization of Carbon and Silicon Cluster Geometry for Tersoff Potential using Differential Evolution; M.M. Ali, A. Törn. D.C. Programming Approach for