Computational Design of Ligand Binding Proteins / edited by Barry L. Stoddard.

Format:

Book

Contributor:

Stoddard, Barry L., editor.

SpringerLink (Online service)

Series:

Methods in molecular biology 1064-3745 ; 1414.

Methods in Molecular Biology, 1064-3745 ; 1414

Language:

English

Subjects (All):

Life sciences.

Proteins.

Physical Description:

1 online resource (XVI, 375 pages) : 94 illustrations, 76 illustrations in color.

Contained In:

Springer eBooks

Place of Publication:

New York, NY : Springer New York : Imprint: Humana Press, 2016.

System Details:

text file PDF

Summary:

This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Contents:

In silico Identification and Characterization of Protein-Ligand Binding Sites

Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities

Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers

Rosetta and the Design of Ligand Binding Sites

PocketOptimizer and the Design of Ligand Binding Sites

Proteus and the Design of Ligand Binding Sites

A Structure Based Design Protocol for Optimizing Combinatorial Protein Libraries

Combined and Iterative Use of Computational Design and Directed Evolution for Protein-Ligand Binding Design

Improving Binding Affinity and Selectivity of Computationally Designed Ligand Binding Proteins Using Experiments

Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids

De Novo Design of Metalloproteins and Metalloenzymes in a Three-helix Bundle

Design of Light-Controlled Protein Conformations and Functions

Computational Introduction of Catalytic Activity into Proteins

Generating High Accuracy Peptide Binding Data in High Throughput with Yeast Surface Display and SORTCERY

Design of Specific Peptide-Protein Recognition

Computational Design of DNA-binding Proteins

Motif-driven Design of Protein-Protein Interfaces

Computational Reprogramming of T Cell Antigen Receptor Binding Properties

Computational Modeling of T Cell Receptor Complexes

Computational Design of Protein Linkers

Modeling of Protein-RNA Complex Structures Using Computational Docking Methods.

Other Format:

Printed edition:

ISBN:

9781493935697

Access Restriction:

Restricted for use by site license.