Ebook: Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches

Optimization in Computational Chemistry and Molecular Biology:Local and Global Approaches covers recent developments in optimization techniques for addressing several computational chemistry and biology problems. A tantalizing problem that cuts across the fields of computational chemistry, biology, medicine, engineering and applied mathematics is how proteins fold. Global and local optimization provide a systematic framework of conformational searches for the prediction of three-dimensional protein structures that represent the global minimum free energy, as well as low-energy biomolecular conformations.
Each contribution in the book is essentially expository in nature, but of scholarly treatment. The topics covered include advances in local and global optimization approaches for molecular dynamics and modeling, distance geometry, protein folding, molecular structure refinement, protein and drug design, and molecular and peptide docking.
Audience: The book is addressed not only to researchers in mathematical programming, but to all scientists in various disciplines who use optimization methods in solving problems in computational chemistry and biology.

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Optimization in Computational Chemistry and Molecular Biology:Local and Global Approaches covers recent developments in optimization techniques for addressing several computational chemistry and biology problems. A tantalizing problem that cuts across the fields of computational chemistry, biology, medicine, engineering and applied mathematics is how proteins fold. Global and local optimization provide a systematic framework of conformational searches for the prediction of three-dimensional protein structures that represent the global minimum free energy, as well as low-energy biomolecular conformations.
Each contribution in the book is essentially expository in nature, but of scholarly treatment. The topics covered include advances in local and global optimization approaches for molecular dynamics and modeling, distance geometry, protein folding, molecular structure refinement, protein and drug design, and molecular and peptide docking.
Audience: The book is addressed not only to researchers in mathematical programming, but to all scientists in various disciplines who use optimization methods in solving problems in computational chemistry and biology.

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Optimization in Computational Chemistry and Molecular Biology:Local and Global Approaches covers recent developments in optimization techniques for addressing several computational chemistry and biology problems. A tantalizing problem that cuts across the fields of computational chemistry, biology, medicine, engineering and applied mathematics is how proteins fold. Global and local optimization provide a systematic framework of conformational searches for the prediction of three-dimensional protein structures that represent the global minimum free energy, as well as low-energy biomolecular conformations.
Each contribution in the book is essentially expository in nature, but of scholarly treatment. The topics covered include advances in local and global optimization approaches for molecular dynamics and modeling, distance geometry, protein folding, molecular structure refinement, protein and drug design, and molecular and peptide docking.
Audience: The book is addressed not only to researchers in mathematical programming, but to all scientists in various disciplines who use optimization methods in solving problems in computational chemistry and biology.
Content:
Front Matter....Pages i-vii
Predicting Protein Tertiary Structure using a Global Optimization Algorithm with Smoothing....Pages 1-18
Methodology for Elucidating the Folding Dynamics of Peptides : Met-enkephalin Case Study....Pages 19-46
Energy Landscape Projections of Molecular Potential Functions....Pages 47-55
Global Optimization and Sampling in the Context of Tertiary Structure Prediction: A Comparison of Two Algorithms....Pages 57-71
Protein Folding Simulations by Monte Carlo Simulated Annealing and Multicanonical Algorithm....Pages 73-90
Thermodynamics of Protein Folding — The Generalized-Ensemble Approach....Pages 91-105
An approach to detect the dominant folds of proteinlike heteropolymers from the statistics of a homopolymeric chain....Pages 107-129
Gene Sequences are Locally Optimized for Global mRNA Folding....Pages 131-140
Structure Calculations of Symmetric Dimers using Molecular Dynamics/Simulated Annealing and NMR Restraints: The Case of the RII? Subunit of Protein Kinase A....Pages 141-156
Structure Prediction of Binding Sites of MHC Class II Molecules based on the Crystal of HLA-DRB1 and Global Optimization....Pages 157-189
A Coupled Scanning and Optimization Scheme for Analyzing Molecular Interactions....Pages 191-207
Improved Evolutionary Hybrids for Flexible Ligand Docking in AutoDock....Pages 209-229
Electrostatic Optimization in Ligand Complementarity and Design....Pages 231-242
Exploring potential solvation sites of proteins by multistart local minimization....Pages 243-261
On relative position of two biopolymer molecules minimizing the weighted sum of interatomic distances squared....Pages 263-266
Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization....Pages 267-286
Optimization of Carbon and Silicon Cluster Geometry for Tersoff Potential using Differential Evolution....Pages 287-300
D.C. Programming Approach for Large-Scale Molecular Optimization via the General Distance Geometry Problem....Pages 301-339
Back Matter....Pages 341-342

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Optimization in Computational Chemistry and Molecular Biology:Local and Global Approaches covers recent developments in optimization techniques for addressing several computational chemistry and biology problems. A tantalizing problem that cuts across the fields of computational chemistry, biology, medicine, engineering and applied mathematics is how proteins fold. Global and local optimization provide a systematic framework of conformational searches for the prediction of three-dimensional protein structures that represent the global minimum free energy, as well as low-energy biomolecular conformations.
Each contribution in the book is essentially expository in nature, but of scholarly treatment. The topics covered include advances in local and global optimization approaches for molecular dynamics and modeling, distance geometry, protein folding, molecular structure refinement, protein and drug design, and molecular and peptide docking.
Audience: The book is addressed not only to researchers in mathematical programming, but to all scientists in various disciplines who use optimization methods in solving problems in computational chemistry and biology.
Content:
Front Matter....Pages i-vii
Predicting Protein Tertiary Structure using a Global Optimization Algorithm with Smoothing....Pages 1-18
Methodology for Elucidating the Folding Dynamics of Peptides : Met-enkephalin Case Study....Pages 19-46
Energy Landscape Projections of Molecular Potential Functions....Pages 47-55
Global Optimization and Sampling in the Context of Tertiary Structure Prediction: A Comparison of Two Algorithms....Pages 57-71
Protein Folding Simulations by Monte Carlo Simulated Annealing and Multicanonical Algorithm....Pages 73-90
Thermodynamics of Protein Folding — The Generalized-Ensemble Approach....Pages 91-105
An approach to detect the dominant folds of proteinlike heteropolymers from the statistics of a homopolymeric chain....Pages 107-129
Gene Sequences are Locally Optimized for Global mRNA Folding....Pages 131-140
Structure Calculations of Symmetric Dimers using Molecular Dynamics/Simulated Annealing and NMR Restraints: The Case of the RII? Subunit of Protein Kinase A....Pages 141-156
Structure Prediction of Binding Sites of MHC Class II Molecules based on the Crystal of HLA-DRB1 and Global Optimization....Pages 157-189
A Coupled Scanning and Optimization Scheme for Analyzing Molecular Interactions....Pages 191-207
Improved Evolutionary Hybrids for Flexible Ligand Docking in AutoDock....Pages 209-229
Electrostatic Optimization in Ligand Complementarity and Design....Pages 231-242
Exploring potential solvation sites of proteins by multistart local minimization....Pages 243-261
On relative position of two biopolymer molecules minimizing the weighted sum of interatomic distances squared....Pages 263-266
Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization....Pages 267-286
Optimization of Carbon and Silicon Cluster Geometry for Tersoff Potential using Differential Evolution....Pages 287-300
D.C. Programming Approach for Large-Scale Molecular Optimization via the General Distance Geometry Problem....Pages 301-339
Back Matter....Pages 341-342
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