Reviews in computational chemistry . 28 / / edited by Abby L. Parrill, Kenny B. Lipkowitz

• Pubblicazione: Hoboken, New Jersey : , : Wiley, , [2015]; ©2015
• Descrizione fisica: 1 online resource (570 p.)
• Disciplina: 542.8/5
• Soggetto topico: Chemistry - Data processing; Chemistry - Mathematics
• Persona (resp. second.): ParrillAbby L.; LipkowitzKenny B.
• Note generali: Description based upon print version of record.
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: Cover; Title Page; Copyright; Contents; Preface; List of Contributors; Contributors to Previous Volumes; Chapter 1 Free-Energy Calculations with Metadynamics: Theory and Practice; Introduction; Molecular Dynamics and Free-Energy Estimation; Molecular Dynamics; Free-Energy Landscapes; A Toy Model: Alanine Dipeptide; Biased Sampling; Adaptive Biasing with Metadynamics; Reweighting; Well-Tempered Metadynamics; Reweighting; Metadynamics How-To; The Choice of the CV(s); The Width of the Deposited Gaussian Potential; The Deposition Rate of the Gaussian Potential ; A First Test Run Using Gyration RadiusA Better Collective Variable: Φ Dihedral Angle; Well-Tempered Metadynamics Using Gyration Radius; Well-Tempered Metadynamics Using Dihedral Angle Φ; Advanced Collective Variables; Path-Based Collective Variables; Collective Variables Based on Dimensional Reduction Methods; Template-Based Collective Variables; Potential Energy as a Collective Variable; Improved Variants; Multiple Walkers Metadynamics; Replica Exchange Metadynamics; Bias Exchange Metadynamics; Adaptive Gaussians; Conclusion; Acknowledgments; Appendix A: Metadynamics Input Files with PLUMED ; ReferencesChapter 2 Polarizable Force Fields for Biomolecular Modeling; Introduction; Modeling Polarization Effects; Induced Dipole Models; Classic Drude Oscillators; Fluctuating Charges; Recent Developments; AMOEBA; SIBFA; NEMO; CHARMM-Drude; CHARMM-FQ; X-Pol; PFF; Applications; Water Simulations; Ion Solvation; Small Molecules; Proteins; Lipids; Continuum Solvents for Polarizable Biomolecular Solutes; Macromolecular X-ray Crystallography Refinement; Prediction of Organic Crystal Structure, Thermodynamics, and Solubility; Summary; Acknowledgment; References ; Chapter 3 Modeling Protein Folding PathwaysIntroduction; Outline of this Chapter; Protein Simulation Methodology; Force Fields, Models and Solvation Approaches; Unfolding: The Reverse of Folding; Elevated Temperature Unfolding Simulations; Biological Relevance of Forced Unfolding; Biased or Restrained MD; Characterizing Different States; Protein Folding and Refolding; Folding in Families; Conclusions and Outlook; Acknowledgment; References; Chapter 4 Assessing Structural Predictions of Protein-Protein Recognition: The CAPRI Experiment; Introduction; Protein-Protein Docking ; A Short History of Protein-Protein DockingMajor Current Algorithms; The CAPRI Experiment; Why Do Blind Predictions?; Organizing CAPRI; The CAPRI Targets; Creating a Community; Assessing Docking Predictions; The CAPRI Evaluation Procedure; A Survey of the Results of 12 Years of Blind Predictions on 45 Targets; Recent Developments in Modeling Protein-Protein Interaction; Modeling Multicomponent Assemblies. The Multiscale Approach; Genome-Wide Modeling of Protein-Protein Interaction; Engineering Interactions and Predicting Affinity; Conclusion; Acknowledgments; References ; Chapter 5 Kinetic Monte Carlo Simulation of Electrochemical Systems
• Sommario/riassunto: The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include: Free-energy Calculations with Metadynamics Polarizable Force Fields for Biomolecular Modeling Modeling Protei
• Titolo autorizzato: Reviews in computational chemistry
• ISBN: 1-118-88993-2; 1-118-88988-6
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Lingua di pubblicazione: Inglese
• Record Nr.: 9910830676903321
• Lo trovi qui: Univ. Federico II
• Serie: Reviews in Computational Chemistry