Provides step-by-step protocols presented by world renowned experts in the field
Contains authoritative reviews of methods applicable to protein modeling
Enables readers to apply state-of-the-art methods to their own research
Contains links to downloadable software made available by the authors
Provides step-by-step protocols presented by world renowned experts in the field
Contains authoritative reviews of methods applicable to protein modeling
Enables readers to apply state-of-the-art methods to their own research
Contains links to downloadable software made available by the authors
Includes supplementary material: sn.pub/extras
Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists – especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, the book is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics. Links to downloadable software made available by the authors are also provided.
Methodology 1 Molecular dynamics simulationsErik R. Lindahl 2 Monte Carlo simulationsMichael W. Deem, David J. Earl 3 Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymesJiali Gao, Dan. T. Major, Yao Fan, Yen-lin Lin, Shuhua Ma and Kin-Yiu Wong 4 Comparison of forcefields for molecular dynamics simulationsOlgun Guvench and Alexander D. MacKerell, Jr. 5 Normal modes and essential dynamicsSteven Hayward and Bert L. de Groot Free energy calculations 6 Calculation of absolute protein-ligand binding constants with the molelcular dynamics free energy perturbation methodHyung-June Woo 7 Free energy calculations applied to membrane proteinsChristophe Chipot Molecular modeling of membrane proteins 8 Molecular dynamics simulations of membrane proteinsPhilip C. Biggin and Peter J. Bond 9 Membrane associated proteins and peptidesMark F. Lensink 10 Implicit membrane models for membrane protein simulationMichael Feig Protein structure determination 11 Comparative Modeling of ProteinsGerald H. Lushington 12 Transmembrane protein models based on high throughput MD simulations with experimental constraintsAndrew J. Beevers, Andreas Kukol 13 NMR-based modelling and refinement of protein 3D structures and their complexesG Fuentes, A.D.J. van Dijk and Alexandre M.J.J. Bonvin Conformational change 14 Conformational changes in protein functionHaiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, and Yong Duan 15 Protein folding and unfolding by all-atom molecular dynamics simulationsHongxing Lei and Yong Duan 16 Modeling of protein misfolding in diseaseEdyta B. Malolepsza Applications to drug design 17 IdentifyingPutative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and DockingDavid S. Wishart 18 Receptor flexibility for large scale in-silico ligand screens: chances and challengesB. Fisher, H. Merlitz and Wolfgang Wenzel 19 Molecular dockingGarrett M. Morris and Marguerita Lim-Wilby
From the reviews:
"This book covers many different aspects of protein modeling and is just one volume in an extremely large series ... . might be useful as an overview of the various techniques and methods used for the molecular modeling of proteins." (Andrzej Kloczkowski and Robert L. Jernigan, Journal of the American Chemical Society, Vol. 130 (37), 2008)
Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. Molecular Modeling of Proteins provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists - especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in this book, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, Molecular Modeling of Proteins is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics.
Methodology.- Molecular Dynamics Simulations.- Monte Carlo Simulations.- Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes.- Comparison of Protein Force Fields for Molecular Dynamics Simulations.- Normal Modes and Essential Dynamics.- Free Energy Calculations.- Calculation of Absolute Protein-Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method.- Free Energy Calculations Applied to Membrane Proteins.- Molecular Modeling of Membrane Proteins.- Molecular Dynamics Simulations of Membrane Proteins.- Membrane-Associated Proteins and Peptides.- Implicit Membrane Models for Membrane Protein Simulation.- Protein Structure Determination.- Comparative Modeling of Proteins.- Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints.- Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes.- Conformational Change.- Conformational Changes in Protein Function.- Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations.- Modeling of Protein Misfolding in Disease.- Applications to Drug Design.- Identifying Putative Drug Targets and Potential Drug Leads.- Receptor Flexibility for Large-Scale In Silico Ligand Screens.- Molecular Docking.
From the reviews:
"This book covers many different aspects of protein modeling and is just one volume in an extremely large series ... . might be useful as an overview of the various techniques and methods used for the molecular modeling of proteins." (Andrzej Kloczkowski and Robert L. Jernigan, Journal of the American Chemical Society, Vol. 130 (37), 2008)
Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists - especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, the book is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics. Links to downloadable software made available by the authors are also provided.
Inhaltsverzeichnis
Methodology 1 Molecular dynamics simulationsnErik R. Lindahl 2 Monte Carlo simulationsnMichael W. Deem, David J. Earl 3 Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymesnJiali Gao, Dan. T. Major, Yao Fan, Yen-lin Lin, Shuhua Ma and Kin-Yiu Wong 4 Comparison of forcefields for molecular dynamics simulationsnOlgun Guvench and Alexander D. MacKerell, Jr. 5 Normal modes and essential dynamicsnSteven Hayward and Bert L. de Groot Free energy calculations 6 Calculation of absolute protein-ligand binding constants with the molelcular dynamics free energy perturbation methodnHyung-June Woo 7 Free energy calculations applied to membrane proteinsnChristophe Chipot Molecular modeling of membrane proteins 8 Molecular dynamics simulations of membrane proteinsnPhilip C. Biggin and Peter J. Bond 9 Membrane associated proteins and peptidesnMark F. Lensink 10 Implicit membrane models for membrane protein simulationnMichael Feig Protein structure determination 11 Comparative Modeling of ProteinsnGerald H. Lushington 12 Transmembrane protein models based on high throughput MD simulations with experimental constraintsnAndrew J. Beevers, Andreas Kukol 13 NMR-based modelling and refinement of protein 3D structures and their complexesnG Fuentes, A.D.J. van Dijk and Alexandre M.J.J. Bonvinn Conformational change 14 Conformational changes in protein functionnHaiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, and Yong Duan 15 Protein folding and unfolding by all-atom molecular dynamics simulationsnHongxing Lei and Yong Duan 16 Modeling of protein misfolding in diseasenEdyta B. Malolepsza Applications to drug design 17 IdentifyingPutative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and DockingnDavid S. Wishart 18 Receptor flexibility for large scale in-silico ligand screens: chances and challengesnB. Fisher, H. Merlitz and Wolfgang Wenzel 19 Molecular dockingnGarrett M. Morris and Marguerita Lim-Wilby
Klappentext
Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. Molecular Modeling of Proteins provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists ¿ especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in this book, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, Molecular Modeling of Proteins is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics.
Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists - especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, the book is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics. Links to downloadable software made available by the authors are also provided.
