Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Jun 23, 2026

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

Automated scaffold selection for enzyme design.

Christoph Malisi¹, Oliver Kohlbacher, Birte Höcker

¹Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

|May 2, 2009

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Interacting Species Database (ISDB): comprehensive resource for interspecies interactions at the molecular level.

Bioinformatics (Oxford, England)·2026

Same author

Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.

Nature chemical biology·2026

Same author

Meet NUM-ENRICH: A Collaborative National Effort to Extend and Harmonize Research Infrastructures Within the German Network University Medicine.

Studies in health technology and informatics·2026

Same author

Enabling Privacy-Preserving Federated Learning in Healthcare: The FLAME Architecture and Policy Framework.

Studies in health technology and informatics·2026

Same author

A Maturity Model for the Enforcement of PETs in Federated Settings.

Studies in health technology and informatics·2026

Same author

Clinical outcome of biomarker-guided therapies in adult neuro-oncology patients: An update from the Tübingen molecular tumor board cohort.

Neuro-oncology advances·2026

Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026

Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026

Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026

Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026

Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026

Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026

See all related articles

Computational protein design uses ScaffoldSelection to find suitable protein scaffolds for novel enzymatic functions. This algorithm rapidly identifies attachment sites for catalytic residues, aiding in the creation of new proteins.

Area of Science:

* Computational biology
* Protein engineering
* Bioinformatics

Background:

* Designing novel protein functions on existing scaffolds is a key goal in computational protein design.
* Identifying suitable protein scaffolds for specific catalytic residues and their spatial arrangement is crucial for this process.

Purpose of the Study:

* To present ScaffoldSelection, an algorithm for rapidly searching protein structures to identify potential attachment sites for enzymatic motifs.
* To enable the selection of appropriate protein scaffolds for hosting predefined catalytic residues and supporting specific chemical reactions.

Main Methods:

* ScaffoldSelection identifies potential attachment sites by first locating pairs of backbone positions in pocket-like regions.
* It then uses a graph-theoretical approach to combine these pairs into complete attachment sites.

More Related Videos

Protein Engineering by Yeast Surface Display

Protein Engineering by Yeast Surface Display

Published on: November 29, 2024

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

Published on: October 24, 2011

Related Experiment Videos

Last Updated: Jun 23, 2026

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

Protein Engineering by Yeast Surface Display

Protein Engineering by Yeast Surface Display

Published on: November 29, 2024

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

Published on: October 24, 2011

* The algorithm assesses identified sites for their ability to accommodate substrates or transition states.

Main Results:

* Searching approximately 3500 Protein Data Bank structures identified suitable backbone geometries for 12 chemical reactions.
* The native active site geometry was accurately recapitulated in all 12 test cases, ranking in the top percentile for 5.
* ScaffoldSelection demonstrated high accuracy and significantly improved speed compared to other methods.

Conclusions:

* ScaffoldSelection is a fast and efficient algorithm for identifying suitable protein scaffolds for computational protein design.
* It aids in preselecting scaffolds for specific reaction types and the introduction of amino acid motifs.
* The algorithm facilitates the construction of novel protein functions on existing scaffolds.