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Protein Engineering

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Cover of 'Protein Engineering'

Table of Contents

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    Book Overview
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    Chapter 1 Protein Engineering: Past, Present, and Future
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    Chapter 2 Rational and Semirational Protein Design
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    Chapter 3 Computational Analysis of Protein Tunnels and Channels
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    Chapter 4 YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations
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    Chapter 5 A Computational Library Design Protocol for Rapid Improvement of Protein Stability: FRESCO
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    Chapter 6 Directed Evolution of Proteins Based on Mutational Scanning
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    Chapter 7 A Brief Guide to the High-Throughput Expression of Directed Evolution Libraries
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    Chapter 8 Library Growth and Protein Expression: Optimal and Reproducible Microtiter Plate Expression of Recombinant Enzymes in E. coli Using MTP Shakers
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    Chapter 9 Normalized Screening of Protein Engineering Libraries by Split-GFP Crude Cell Extract Quantification
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    Chapter 10 Functional Analysis of Membrane Proteins Produced by Cell-Free Translation
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    Chapter 11 Practical Considerations Regarding the Choice of the Best High-Throughput Assay
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    Chapter 12 High-Throughput Screening Assays for Lipolytic Enzymes
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    Chapter 13 Continuous High-Throughput Colorimetric Assays for α -Transaminases
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    Chapter 14 Colorimetric High-Throughput Screening Assays for the Directed Evolution of Fungal Laccases
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    Chapter 15 Directed Coevolution of Two Cellulosic Enzymes in Escherichia coli Based on Their Synergistic Reactions
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    Chapter 16 Program-Guided Design of High-Throughput Enzyme Screening Experiments and Automated Data Analysis/Evaluation
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    Chapter 17 Solid-Phase Agar Plate Assay for Screening Amine Transaminases
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    Chapter 18 Ultrahigh-Throughput Screening of Single-Cell Lysates for Directed Evolution and Functional Metagenomics
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    Chapter 19 Isolation of pH-Sensitive Antibody Fragments by Fluorescence-Activated Cell Sorting and Yeast Surface Display
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    Chapter 20 Library Generation and Auxotrophic Selection Assays in Escherichia coli and Thermus thermophilus
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    Chapter 21 Erratum to: Functional Analysis of Membrane Proteins Produced by Cell-Free Translation
Attention for Chapter 4: YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations
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Chapter title
YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations
Chapter number 4
Book title
Protein Engineering
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7366-8_4
Pubmed ID
Book ISBNs
978-1-4939-7364-4, 978-1-4939-7366-8

Henrik Land, Maria Svedendahl Humble, Land, Henrik, Humble, Maria Svedendahl


In biocatalysis, structural knowledge regarding an enzyme and its substrate interactions complements and guides experimental investigations. Structural knowledge regarding an enzyme or a biocatalytic reaction system can be generated through computational techniques, such as homology- or molecular modeling. For this type of computational work, a computer program developed for molecular modeling of proteins is required. Here, we describe the use of the program YASARA Structure. Protocols for two specific biocatalytic applications, including both homology modeling and molecular modeling such as energy minimization, molecular docking simulations and molecular dynamics simulations, are shown. The applications are chosen to give realistic examples showing how structural knowledge through homology and molecular modeling is used to guide biocatalytic investigations and protein engineering studies.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 341 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 341 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 53 16%
Student > Master 39 11%
Student > Ph. D. Student 33 10%
Researcher 21 6%
Unspecified 12 4%
Other 41 12%
Unknown 142 42%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 70 21%
Agricultural and Biological Sciences 33 10%
Chemistry 26 8%
Pharmacology, Toxicology and Pharmaceutical Science 16 5%
Unspecified 10 3%
Other 33 10%
Unknown 153 45%