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Computational Design of Ligand Binding Proteins

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Cover of 'Computational Design of Ligand Binding Proteins'

Table of Contents

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    Book Overview
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    Chapter 1 In silico Identification and Characterization of Protein-Ligand Binding Sites
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    Chapter 2 Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities.
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    Chapter 3 Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers.
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    Chapter 4 Computational Design of Ligand Binding Proteins
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    Chapter 5 PocketOptimizer and the Design of Ligand Binding Sites.
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    Chapter 6 Proteus and the Design of Ligand Binding Sites.
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    Chapter 7 A Structure-Based Design Protocol for Optimizing Combinatorial Protein Libraries.
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    Chapter 8 Computational Design of Ligand Binding Proteins
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    Chapter 9 Computational Design of Ligand Binding Proteins
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    Chapter 10 Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids.
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    Chapter 11 De Novo Design of Metalloproteins and Metalloenzymes in a Three-Helix Bundle.
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    Chapter 12 Design of Light-Controlled Protein Conformations and Functions.
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    Chapter 13 Computational Introduction of Catalytic Activity into Proteins.
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    Chapter 14 Computational Design of Ligand Binding Proteins
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    Chapter 15 Design of Specific Peptide-Protein Recognition.
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    Chapter 16 Computational Design of DNA-Binding Proteins.
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    Chapter 17 Motif-Driven Design of Protein-Protein Interfaces.
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    Chapter 18 Computational Design of Ligand Binding Proteins
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    Chapter 19 Computational Design of Ligand Binding Proteins
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    Chapter 20 Computational Design of Protein Linkers.
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    Chapter 21 Modeling of Protein-RNA Complex Structures Using Computational Docking Methods.
Attention for Chapter 20: Computational Design of Protein Linkers.
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Chapter title
Computational Design of Protein Linkers.
Chapter number 20
Book title
Computational Design of Ligand Binding Proteins
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-3569-7_20
Pubmed ID
Book ISBNs
978-1-4939-3567-3, 978-1-4939-3569-7
Authors

Brian Kuhlman, Tim Jacobs, Tom Linskey

Editors

Barry L. Stoddard

Abstract

Naturally occurring proteins often consist of multiple distinct domains joined by linker regions. Similarly, the ability to combine globular protein domains through engineered linkers would allow the creation of a wide variety of complex and useful multifunctional proteins. Recent advances in computational design of protein structures have enabled highly accurate design of novel protein structures. In this chapter we outline a computational protocol for the de novo design of protein linkers, and apply this protocol to the design of a helical linker between two rigid protein domains.

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Mendeley readers

The data shown below were compiled from readership statistics for 12 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 12 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 5 42%
Researcher 2 17%
Student > Master 2 17%
Unknown 3 25%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 33%
Chemistry 2 17%
Pharmacology, Toxicology and Pharmaceutical Science 1 8%
Neuroscience 1 8%
Agricultural and Biological Sciences 1 8%
Other 0 0%
Unknown 3 25%