Manual for state-of-the-art concepts and methodologies, as well as an advanced, specialized tool to design novel and orignial research for public health
Provides step-by-step detail essential for reproducible results
Contains key notes and implementaion advice from the experts
Due to the rapid and steady growth of available low-cost computer power, the use of computers for discovering and designing new drugs is becoming a central topic in modern molecular biology and medicinal chemistry. In Computational Drug Discovery and Design: Methods and Protocols expert researchers in the field provide key techniques to investigate biomedical applications for drug developments based on computational chemistry. These include methods and techniques from binding sites prediction to the accurate inclusion of solvent and entropic effects, from high-throughput screening of large compound databases to the expanding area of protein-protein inhibition, toward quantitative free-energy approaches in ensemble-based drug design using distributed computing. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, reference to software and open source analysis tools, step-by-step, readily reproducible computational protocols, and key tips on troubleshooting and avoiding known pitfalls.
Thorough and intuitive, Computational Drug Discovery and Design: Methods and Protocols aids scientists in the continuing study of state-of-the-art concepts and computer-based methodologies.
Part I: Drug Binding Site Prediction, Design, and Deillegalscriptors
1. A Molecular Dynamics Ensemble-based Approach for the Mapping of Druggable Binding Sites
Anthony Ivetac and J, Andrew McCammon
2. Analysis of Protein Binding Sites by Computational Solvent Mapping
David R. Hall, Dima Kozakov, and Sandor Vajda
3. Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
Angela Wilkins, Serkan Erdin, Rhonald Lua, and Olivier Lichtarge
4. Information Entropic Function for Molecular Deillegalscriptor Profiling
Anne Mai Wasswrmann, Britta Nisius, Martin Vogt, and
Jürgen Bajorath
Part II: Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
5. Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
Guray Kuzu, Ozlem Keskin, Attila Gursoy, and Ruth Nussinov
6. Flexibility Analysis of Biomacromolecules with Application to Computer-aided Drug Design
Simone Fulle and Holger Gohlke
7.On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
Sara Nichols, Riccardo Baron, and J. Andrew McCammon
8. Virtual Ligand Screening Against Comparative Protein Structure Models
Hao Fan, John J. Irwin, and Andrej Sali
9.AMMOS Software: Method and Application
Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O. Villoutreix, and Maria A. Miteva
10.Rosetta Ligand Docking with Flexible XML Protocols
Gordon Lemmon and Jens Meiler
11.Normal Mode-Based Approaches in Receptor Ensemble Docking
Claudio N. Cavasotto
12. Application of Conformational Clustering in Protein-Ligand Docking
Giovanni Bottegoni, Walter Rocchia, and Andrea Cavalli
13. How to Benchmark Methods for Structure-based Virtual Screenin of Large Compound Libraries
Andrew J. Christofferson and Niu Huang
Part III: Prediction of Protein-Protein Docking and Interactions
14. AGGRESCAN: Method, Application, and Perspectives for Drug Design
Natalia S. de Groot, Virginia Castillo, Ricardo Graña, and Salvador Ventura Zamora
15. ATTRACT and PTOOLS: Open Source Programs for Protein-protein Docking
Sebastian Schneider, Adrien Saladin, Chantal Prevost, and Martin Zacharias
16. Prediction of Interacting Protein Residues using Sequence and Structure Data
Vedran Franke, Mile Sikic, and Kristian Vlahovicek
Part IV: Rescoring Docking Predictions
17. MM-GB/SA Rescoring of Docking Poses
Cristiano R.W. Guimarães
18. A Case Study of Scoring and Rescoring in Peptide Docking
Zunnan Huang and Chung Wong
19. The Solvated Interaction Energy (SIE) Method for Scoring Binding Affinities
Traian Sulea and Enrico Purisima
20. Linear Interaction Energy (LIE): Method and Applications in Drug Design
Hugo Guitiérrez-de-Terán and Johan Åqvist
Part V: Crucial Neglected Effects: Entropy, Solvent, and Protonation
21. Estimation of Conformational Entropy in Protein-Ligand Interactions: A Computational Prespective
Anton Polyansky, Ruben Zubac, and Bojan Zagrovic
22. Explicit Treatment of Water Molecules in Data-driven Protein-protein Docking: The Solvated HADDOCKing Approach
Panagotis L. Kastritis, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin
23. Protein–water Interactions in MD Simulations: POPS/POPSCOMP Solvent Accessibility Analysis, Solvation Forces and Hydration Sites
Arianna Fornili, Flavia Autore, Nesrine Chakroun, Pierre Martinez, and Franca Fraternali
24. Computing the Thermodynamic Contributions of Interfacial Water
Zheng Li and Themis Lazaridis
25. Assignment of Protonation States in Proteins and Ligands: Combining pKa Prediction with Hydrogen Bonding Network Optimization
Elmar Krieger, Rob Hooft, Roland Dunbrack, and Barbara Krieger
Part VI: Toward the Use of Robust Free Energy Methods in Drug Design
26. Best Practices in Free Energy Calculations for Drug Design
Michael Shirts
27. Independent-Trajectory Thermodynamic Integration:
A Practical Guide to Protein-Drug Binding Free
Energy Calculations Using Distributed Computing
Morgan Lawrenz, Riccardo Baron, Yi Wang, and J. Andrew McCammon
28. Free Energy Calculations from One-step Perturbations
Chris Oostenbrink
29. Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions
Neva Beker and Francesco L. Gervasio
30. Accelerated Molecular Dynamics In Computational Drug Design
Jeff Wereszczynski and J. Andrew McCammon
Part VII: Biomedical Applications
31. Molecular Dynamics Applied in Drug Discovery: the Case of HIV-1 Protease
Yi Shang and Carlos Simmerling
32. Decomposing the Energetic Impact of Drug-Resistant Mutations: The Example of HIV-1 Protease-DRV Binding
Yufeng Cai and Celia Schiffer
33. Virtual Screening Helps Experiment Design: Application to the Akt Phosphatase PHLPP
Bill Sinko, Emma Sierecki, Cesar A.F. de Oliveira, and J. Andrew McCammon
34. Molecular-Level Simulation of Pandemic Influenza Glycoproteins
Rommie Amaro and Wilfred W. Li
35. Homology Modeling of Cannabinoid Receptor: Discovery of Cannabinoid Analogues for Therapeutic Use
Chia-en Chang, Rizi Ai, Michael Gutierrez, and Michael J. Marsella
36. High-throughput Virtual Screening Lead to Discovery of Non-peptidic Inhibitors of West Nile Virus NS3 Protease
Danzhi Huang
From the reviews:
"Given that computational drug design is a rapidly expanding area of research, this book fills a niche that makes it useful for both novices and the more experienced in the field. ... this is a practical manual, refitted with many protocols and examples, of how to employ the new techniques being developed by experts in the expanding field of computational drug discovery.” (Jed N. Lampe, Doody´s Book Reviews, July, 2012)
This Methods in Molecular Biology(TM) volume offers protocols for investigating biomedical applications for drug developments based on computational chemistry. Includes step-by-step, readily reproducible computational protocols, and key tips on troubleshooting.
Due to the rapid and steady growth of available low-cost computer power, the use of computers for discovering and designing new drugs is becoming a central topic in modern molecular biology and medicinal chemistry. In Computational Drug Discovery and Design: Methods and Protocols expert researchers in the field provide key techniques to investigate biomedical applications for drug developments based on computational chemistry. These include methods and techniques from binding sites prediction to the accurate inclusion of solvent and entropic effects, from high-throughput screening of large compound databases to the expanding area of protein-protein inhibition, toward quantitative free-energy approaches in ensemble-based drug design using distributed computing. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, reference to software and open source analysis tools, step-by-step, readily reproducible computational protocols, and key tips on troubleshooting and avoiding known pitfalls.
Thorough and intuitive, Computational Drug Discovery and Design: Methods and Protocols aids scientists in the continuing study of state-of-the-art concepts and computer-based methodologies.
A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites.-Analysis of Protein Binding Sites by Computational Solvent Mapping.-Evolutionary Trace for Prediction and Redesign of Protein Functional Sites.- Information Entropic Functions for Molecular Deillegalscriptor Profiling.-Expanding the Conformational Selection Paradigm in Protein-Ligand Docking.-Flexibility Analysis of Biomacromolecules with Application to Computer-aided Drug Design.-On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening.-Virtual Ligand Screening Against Comparative Protein Structure Models.-AMMOS Software: Method and Application.-Rosetta Ligand Docking with Flexible XML Protocols.-Normal Mode-Based Approaches in Receptor Ensemble Docking.-Application of Conformational Clustering in Protein-Ligand Docking.-How to Benchmark Methods for Structure-based Virtual Screening of Large Compound Libraries.-AGGRESCAN: Method, Application, and Perspectives for Drug Design.-ATTRACT and PTOOLS: Open Source Programs for Protein-protein Docking.-Prediction of Interacting Protein Residues using Sequence and Structure Data.-MM-GB/SA Rescoring of Docking Poses.-A Case Study of Scoring and Rescoring in Peptide Docking.-The Solvated Interaction Energy (SIE) Method for Scoring Binding Affinities.-Linear Interaction Energy (LIE): Method and Applications in Drug Design.-Estimation of Conformational Entropy in Protein-Ligand Interactions: a Computational Perspective.-Explicit Treatment of Water Molecules in Data-driven Protein-protein Docking: The Solvated HADDOCKing Approach.Protein-water Interactions in MD Simulations: POPS/POPSCOMP Solvent Accessibility Analysis, Solvation Forces and Hydration Sites.-Computing the Thermodynamic Contributions of Interfacial Water.-Assignment of Protonation States in Proteins and Ligands: Combining pKa Prediction with Hydrogen Bonding Network Optimization.-Best Practices in Free Energy Calculations for DrugDesign.-Independent-Trajectory Thermodynamic Integration:A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing.- Free Energy Calculations from One-step Perturbations.-Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions.-Accelerated Molecular Dynamics In Computational Drug Design.-Molecular Dynamics Applied in Drug Discovery: the Case of HIV-1 Protease.-Decomposing the Energetic Impact of Drug-Resistant Mutations: The Example of HIV-1 Protease-DRV Binding.-Virtual Screening Helps Experiment Design: Application to the Akt Phosphatase PHLPP.- Molecular-Level Simulation of Pandemic Influenza Glycoproteins.-Homology Modeling of Cannabinoid Receptor: Discovery of Cannabinoid Analogues for Therapeutic Use.-High-throughput Virtual Screening Lead to Discovery of Non-peptidic Inhibitors of West Nile Virus NS3 Protease.
From the reviews:
"Given that computational drug design is a rapidly expanding area of research, this book fills a niche that makes it useful for both novices and the more experienced in the field. ... this is a practical manual, refitted with many protocols and examples, of how to employ the new techniques being developed by experts in the expanding field of computational drug discovery." (Jed N. Lampe, Doody's Book Reviews, July, 2012)
Inhaltsverzeichnis
Part I: Drug Binding Site Prediction, Design, and Deillegalscriptors
1. A Molecular Dynamics Ensemble-based Approach for the Mapping of Druggable Binding Sites
Anthony Ivetac and J, Andrew McCammon
2. Analysis of Protein Binding Sites by Computational Solvent Mapping
David R. Hall, Dima Kozakov, and Sandor Vajda
3. Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
Angela Wilkins, Serkan Erdin, Rhonald Lua, and Olivier Lichtarge
4. Information Entropic Function for Molecular Deillegalscriptor Profiling
Anne Mai Wasswrmann, Britta Nisius, Martin Vogt, and
Jürgen Bajorath
Part II: Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
5. Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
Guray Kuzu, Ozlem Keskin, Attila Gursoy, and Ruth Nussinov
6. Flexibility Analysis of Biomacromolecules with Application to Computer-aided Drug Design
Simone Fulle and Holger Gohlke
7.On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
Sara Nichols, Riccardo Baron, and J. Andrew McCammon
8. Virtual Ligand Screening Against Comparative Protein Structure Models
Hao Fan, John J. Irwin, and Andrej Sali
9.AMMOS Software: Method and Application
Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O. Villoutreix, and Maria A. Miteva
10.Rosetta Ligand Docking with Flexible XML Protocols
Gordon Lemmon and Jens Meiler
11.Normal Mode-Based Approaches in Receptor Ensemble Docking
Claudio N. Cavasotto
12. Application of Conformational Clustering in Protein-Ligand Docking
Giovanni Bottegoni, Walter Rocchia, and Andrea Cavalli
13. How to Benchmark Methods for Structure-based Virtual Screenin of Large Compound Libraries
Andrew J. Christofferson and Niu Huang
Part III: Prediction of Protein-Protein Docking and Interactions
14. AGGRESCAN: Method, Application, and Perspectives for Drug Design
Natalia S. de Groot, Virginia Castillo, Ricardo Graña, and Salvador Ventura Zamora
15. ATTRACT and PTOOLS: Open Source Programs for Protein-protein Docking
Sebastian Schneider, Adrien Saladin, Chantal Prevost, and Martin Zacharias
16. Prediction of Interacting Protein Residues using Sequence and Structure Data
Vedran Franke, Mile Sikic, and Kristian Vlahovicek
Part IV: Rescoring Docking Predictions
17. MM-GB/SA Rescoring of Docking Poses
Cristiano R.W. Guimarães
18. A Case Study of Scoring and Rescoring in Peptide Docking
Zunnan Huang and Chung Wong
19. The Solvated Interaction Energy (SIE) Method for Scoring Binding Affinities
Traian Sulea and Enrico Purisima
20. Linear Interaction Energy (LIE): Method and Applications in Drug Design
Hugo Guitiérrez-de-Terán and Johan Åqvist
Part V: Crucial Neglected Effects: Entropy, Solvent, and Protonation
21. Estimation of Conformational Entropy in Protein-Ligand Interactions: A Computational Prespective
Anton Polyansky, Ruben Zubac, and Bojan Zagrovic
22. Explicit Treatment of Water Molecules in Data-driven Protein-protein Docking: The Solvated HADDOCKing Approach
Panagotis L. Kastritis, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin
23. Protein-water Interactions in MD Simulations: POPS/POPSCOMP Solvent Accessibility Analysis, Solvation Forces and Hydration Sites
Arianna Fornili, Flavia Autore, Nesrine Chakroun, Pierre Martinez, and Franca Fraternali
24. Computing the Thermodynamic Contributions of Interfacial Water
Zheng Li and Themis Lazaridis
25. Assignment of Protonation States in Proteins and Ligands: Combining pKa Prediction with Hydrogen Bonding Network Optimization
Elmar Krieger, Rob Hooft, Roland Dunbrack, and Barbara Krieger
Part VI: Toward the Use of Robust Free Energy Methods in Drug Design
26. Best Practices in Free Energy Calculations for Drug Design
Michael Shirts
27. Independent-Trajectory Thermodynamic Integration:
A Practical Guide to Protein-Drug Binding Free
Energy Calculations Using Distributed Computing
Morgan Lawrenz, Riccardo Baron, Yi Wang, and J. Andrew McCammon
28. Free Energy Calculations from One-step Perturbations
Chris Oostenbrink
29. Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions
Neva Beker and Francesco L. Gervasio
30. Accelerated Molecular Dynamics In Computational Drug Design
Jeff Wereszczynski and J. Andrew McCammon
Part VII: Biomedical Applications
31. Molecular Dynamics Applied in Drug Discovery: the Case of HIV-1 Protease
Yi Shang and Carlos Simmerling
32. Decomposing the Energetic Impact of Drug-Resistant Mutations: The Example of HIV-1 Protease-DRV Binding
Yufeng Cai and Celia Schiffer
33. Virtual Screening Helps Experiment Design: Application to the Akt Phosphatase PHLPP
Bill Sinko, Emma Sierecki, Cesar A.F. de Oliveira, and J. Andrew McCammon
34. Molecular-Level Simulation of Pandemic Influenza Glycoproteins
Rommie Amaro and Wilfred W. Li
35. Homology Modeling of Cannabinoid Receptor: Discovery of Cannabinoid Analogues for Therapeutic Use
Chia-en Chang, Rizi Ai, Michael Gutierrez, and Michael J. Marsella
36. High-throughput Virtual Screening Lead to Discovery of Non-peptidic Inhibitors of West Nile Virus NS3 Protease
Danzhi Huang
Klappentext
Due to the rapid and steady growth of available low-cost computer power, the use of computers for discovering and designing new drugs is becoming a central topic in modern molecular biology and medicinal chemistry. In Computational Drug Discovery and Design: Methods and Protocols expert researchers in the field provide key techniques to investigate biomedical applications for drug developments based on computational chemistry. These include methods and techniques from binding sites prediction to the accurate inclusion of solvent and entropic effects, from high-throughput screening of large compound databases to the expanding area of protein-protein inhibition, toward quantitative free-energy approaches in ensemble-based drug design using distributed computing. Written in the highly successful Methods in Molecular Biology¿ series format, chapters include introductions to their respective topics, reference to software and open source analysis tools, step-by-step, readily reproducible computational protocols, and key tips on troubleshooting and avoiding known pitfalls.n nThorough and intuitive, Computational Drug Discovery and Design: Methods and Protocols aids scientists in the continuing study of state-of-the-art concepts and computer-based methodologies.
Manual for state-of-the-art concepts and methodologies, as well as an advanced, specialized tool to design novel and orignial research for public health
Provides step-by-step detail essential for reproducible results
Contains key notes and implementaion advice from the experts
