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…mehr
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.
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 AcidsJie Zheng Carlos Aleman David Zanuy and Ruth Nussinov18. Probing Oligomerized Conformations of Defensin in the MembraneWenxun Gan Dina Schneidman Ning Zhang Buyong Ma and Ruth Nussinov19. Computational Design of Ligand Binding ProteinsChristine E. Tinberg and Sagar D. Khare20. EpiSweep: Computationally-driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity while Maintaining FunctionYoonjoo Choi Deeptak Verma Karl E. Griswold and Chris Bailey-Kellogg21. Computational Tools for Aiding Rational Antibody DesignKonrad Krawczyk James Dunbar and Charlotte M Deane22. Computational Design of Membrane Curvature-Sensing PeptidesArmando Jerome de Jesus and Hang Yin23. Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library DesignWenkang Huang Ruth Nussinov and Jian Zhang
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 AcidsJie Zheng Carlos Aleman David Zanuy and Ruth Nussinov18. Probing Oligomerized Conformations of Defensin in the MembraneWenxun Gan Dina Schneidman Ning Zhang Buyong Ma and Ruth Nussinov19. Computational Design of Ligand Binding ProteinsChristine E. Tinberg and Sagar D. Khare20. EpiSweep: Computationally-driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity while Maintaining FunctionYoonjoo Choi Deeptak Verma Karl E. Griswold and Chris Bailey-Kellogg21. Computational Tools for Aiding Rational Antibody DesignKonrad Krawczyk James Dunbar and Charlotte M Deane22. Computational Design of Membrane Curvature-Sensing PeptidesArmando Jerome de Jesus and Hang Yin23. Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library DesignWenkang Huang Ruth Nussinov and Jian Zhang
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