Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
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 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
Inhaltsverzeichnis
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
Klappentext
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.n n Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
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: sn.pub/extras
