Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: [...]

Part I: Computational Protein Design1. The Framework of Computational Protein DesignIlan Samish2. Achievements and Challenges in Computational Protein DesignIlan Samish3. Production of Computationally Designed Small Soluble- and Membrane-Proteins: Cloning, Expression and PurificationBarsha Tripathy and Rudresh Acharya4. Deterministic Search methods for Computational Protein DesignSeydou Traoré, David Allouche, Isabelle André Thomas Schiex, and Sophie Barbe5. Geometric Potentials for Computational Protein Sequence DesignJie Li and Patrice Koehl 6. Modeling Binding Affinity of Pathological Mutations for Computational Protein DesignMiguel Romero-Durana, Chiara Pallara, Fabian Glaser, and Juan Fernández-Recio7. Multistate Computational Protein Design with Backbone EnsemblesJames A. Davey and Roberto A. Chica8. Integration of Molecular Dynamics Based Predictions into the Optimization of de novo Protein Designs: Limitations and BenefitsHenrique F. Carvalho, Arménio J. M. Barbosa, Ana C. A. Roque, Olga Iranzo, and Ricardo J. F. Branco9. Applications of Normal Mode Analysis Methods in Computational Protein DesignVincent Frappier, Matthieu Chartier, and Rafael NajmanovichPart II: Software of Computational Protein Design Applications10. Computational Protein Design Under a Given backbone Structure with a Statistical Energy FunctionPeng Xiong, Quan Chen, and Haiyan Liu11. Computational Protein Design Through Grafting and StabilizationCheng Zhu, David D. Mowrey, and Nikolay V. Dokholyan12. An Evolution Based Approach to de novo Protein DesignJeffrey R. Brender, David Shultis, Naureen Aslam, and Yang Zhang13. Parallel Computational Protein Design Yichao Zhou, Bruce R. Donald, and Jianyang Zeng14. BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution PatternsQing Wei, David La, and Daisuke Kihara15. OSPREY Predicts Resistance Mutations using Positive and Negative Computational Protein DesignAdegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M. Reeve, Ivelin Georgiev, Amy C. Anderson, and Bruce R. DonaldPart III: Computational Protein Design of Specific Targets16. Evolution-inspired Computational Design of Symmetric ProteinsArnout R.D. Voet, David Simoncini, Jeremy R.H. Tame, and Kam Y. J. Zhang17. A Protocol for the Design of Protein and Peptide Nanostructure Self-assemblies Exploiting Synthetic Amino Acids