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Computational Protein Design

  • Book
  • © 2017

Overview

Editors:
  1. Ilan Samish

    1. Department of Plants and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

    View editor publications

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  • 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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1529)

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Computational Protein Design

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. The Framework of Computational Protein Design

      • Ilan Samish
      Pages 3-19

    3. Achievements and Challenges in Computational Protein Design

      • Ilan Samish
      Pages 21-94

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

      • Barsa Tripathy, Rudresh Acharya
      Pages 95-106

    5. Deterministic Search Methods for Computational Protein Design

      • Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
      Pages 107-123

    6. Geometric Potentials for Computational Protein Sequence Design

      • Jie Li, Patrice Koehl
      Pages 125-138

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

      • Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
      Pages 139-159

    8. Multistate Computational Protein Design with Backbone Ensembles

      • James A. Davey, Roberto A. Chica
      Pages 161-179

    9. 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, Ricardo J. F. Branco
      Pages 181-201

    10. Applications of Normal Mode Analysis Methods in Computational Protein Design

      • Vincent Frappier, Matthieu Chartier, Rafael Najmanovich
      Pages 203-214

  3. Software of Computational Protein Design Applications

    1. Front Matter

      Pages 215-215
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    2. Computational Protein Design Under a Given Backbone Structure with the ABACUS Statistical Energy Function

      • Peng Xiong, Quan Chen, Haiyan Liu
      Pages 217-226

    3. Computational Protein Design Through Grafting and Stabilization

      • Cheng Zhu, David D. Mowrey, Nikolay V. Dokholyan
      Pages 227-241

    4. An Evolution-Based Approach to De Novo Protein Design

      • Jeffrey R. Brender, David Shultis, Naureen Aslam Khattak, Yang Zhang
      Pages 243-264

    5. Parallel Computational Protein Design

      • Yichao Zhou, Bruce R. Donald, Jianyang Zeng
      Pages 265-277

    6. BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns

      • Qing Wei, David La, Daisuke Kihara
      Pages 279-289

    7. 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 et al.
      Pages 291-306

  4. Computational Protein Design of Specific Targets

    1. Front Matter

      Pages 307-307
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    2. Evolution-Inspired Computational Design of Symmetric Proteins

      • Arnout R. D. Voet, David Simoncini, Jeremy R. H. Tame, Kam Y. J. Zhang
      Pages 309-322
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Keywords

About this book

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.

Editors and Affiliations

  • Department of Plants and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

    Ilan Samish

Bibliographic Information

  • Book Title: Computational Protein Design

  • Editors: Ilan Samish

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6637-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2017

  • Hardcover ISBN: 978-1-4939-6635-6Published: 03 December 2016

  • Softcover ISBN: 978-1-4939-8256-1Published: 28 June 2018

  • eBook ISBN: 978-1-4939-6637-0Published: 01 December 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 450

  • Number of Illustrations: 33 b/w illustrations, 111 illustrations in colour

  • Topics: Protein Science

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