Computational Protein Design

ISBN-13: 9781493982561 / Angielski / Miękka / 2018 / 450 str.

Ilan Samish

Spis treści

Part I: Computational Protein Design

1. The Framework of Computational Protein Design

Ilan Samish

2. Achievements and Challenges in Computational Protein Design

Ilan Samish

3. Production of Computationally Designed Small Soluble- and Membrane-Proteins: Cloning, Expression and Purification

Barsha Tripathy and Rudresh Acharya

4. Deterministic Search methods for Computational Protein Design

Seydou Traoré, David Allouche, Isabelle André Thomas Schiex, and Sophie Barbe

5. Geometric Potentials for Computational Protein Sequence Design

Jie Li and Patrice Koehl 

6. Modeling Binding Affinity of Pathological Mutations for Computational Protein Design

Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, and Juan Fernández-Recio

7. Multistate Computational Protein Design with Backbone Ensembles

James A. Davey and Roberto A. Chica

8. Integration of Molecular Dynamics Based Predictions into the Optimization of de novo Protein Designs: Limitations and Benefits

Henrique 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 Design

Vincent Frappier, Matthieu Chartier, and Rafael Najmanovich

Part II: Software of Computational Protein Design Applications

10. Computational Protein Design Under a Given backbone Structure with a Statistical Energy Function

Peng Xiong, Quan Chen, and Haiyan Liu

11. Computational Protein Design Through Grafting and Stabilization

Cheng Zhu, David D. Mowrey, and Nikolay V. Dokholyan

12. An Evolution Based Approach to de novo Protein Design

Jeffrey 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 Patterns

Qing Wei, David La, and Daisuke Kihara

15. OSPREY Predicts Resistance Mutations using Positive and Negative Computational Protein Design

Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M. Reeve, Ivelin Georgiev, Amy C. Anderson, and Bruce R. Donald

Part III: Computational Protein Design of Specific Targets

16. Evolution-inspired Computational Design of Symmetric Proteins

Arnout 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<

Nurit Haspel, Jie Zheng, Carlos Aleman, David Zanuy, and Ruth Nussinov

18. Probing Oligomerized Conformations of Defensin in the Membrane

Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, and Ruth Nussinov

19. Computational Design of Ligand Binding Proteins

Christine E. Tinberg and Sagar D. Khare

20. EpiSweep: Computationally-driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity while Maintaining Function

Yoonjoo Choi, Deeptak Verma, Karl E. Griswold, and Chris Bailey-Kellogg

21. Computational Tools for Aiding Rational Antibody Design

Konrad Krawczyk, James Dunbar, and Charlotte M Deane

22. Computational Design of Membrane Curvature-Sensing Peptides

Armando Jerome de Jesus and Hang Yin

23. Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library Design

Wenkang Huang, Ruth Nussinov, and Jian Zhang

Blurb

The 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.