Description
Book SynopsisThe aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Table of ContentsPart I: Computational Protein Design1. The Framework of Computational Protein DesignIlan Samish
2. Achievements and Challenges in Computational Protein DesignIlan Samish
3. Production of Computationally Designed Small Soluble- and Membrane-Proteins: Cloning, Expression and PurificationBarsha Tripathy and Rudresh Acharya
4. Deterministic Search methods for Computational Protein DesignSeydou Traoré, David Allouche, Isabelle André Thomas Schiex, and Sophie Barbe
5. 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-Recio
7. Multistate Computational Protein Design with Backbone EnsemblesJames A. Davey and Roberto A. Chica
8. 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. Branco
9. 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 Liu
11. Computational Protein Design Through Grafting and StabilizationCheng Zhu, David D. Mowrey, and Nikolay V. Dokholyan
12. An Evolution Based Approach to de novo Protein DesignJeffrey R. Brender, David Shultis, Naureen Aslam, and Yang Zhang
13. Parallel Computational Protein Design Yichao Zhou, Bruce R. Donald, and Jianyang Zeng
14. BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution PatternsQing Wei, David La, and Daisuke Kihara
15. 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. Zhang
17. A Protocol for the Design of Protein and Peptide Nanostructure Self-assemblies Exploiting Synthetic Amino Acids
18. Probing Oligomerized Conformations of Defensin in the MembraneWenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, and Ruth Nussinov
19. Computational Design of Ligand Binding ProteinsChristine E. Tinberg and Sagar D. Khare
20. EpiSweep: Computationally-driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity while Maintaining FunctionYoonjoo Choi, Deeptak Verma, Karl E. Griswold, and Chris Bailey-Kellogg
21. Computational Tools for Aiding Rational Antibody DesignKonrad Krawczyk, James Dunbar, and Charlotte M Deane
22. Computational Design of Membrane Curvature-Sensing PeptidesArmando Jerome de Jesus and Hang Yin
23. Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library DesignWenkang Huang, Ruth Nussinov, and Jian Zhang
