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PROTEIN STABILITY PREDICTION

Accurately predict protein stability resulting from residue-level changes to a protein structure. PRICING DOWNLOAD FREE TRIAL

Use Lasergene Protein’s protein design software to perform essential protein stability predictions in minutes.

Protein stability prediction is essential for optimizing protein functional studies, but many standard approaches to improving solubility and expression are often ineffective due to degradation or thermodynamic instability. Our protein design software, part of Lasergene Protein, includes protein mutation stability prediction tools that use a deterministic protein design algorithm find the global minimum energy conformation (GMEC). This allows you to make changes at the residue-level on a protein structure and predict whether these changes are likely to be stabilizing or destabilizing compared to the original structure, a beneficial process for PCR site-directed mutagenesis. Our protein stability prediction tools also make it easy to search for amino acid positions that are important for protein stability by performing computational alanine scanning or serine scanning to detect hot-spots, residues whose variants destabilize the structure. Use Lasergene Protein’s advanced protein design software to perform accurate protein stability predictions in minutes!

Protein stability prediction in 4 simple steps

Protein Stability Prediction Step 1

Step 1

Choose Modeling>Protein Design to launch the protein design wizard

Protein Stability Prediction Step 2

Step 2

Perform alanine scanning or serine scanning to evaluate residues whose variants impact fold stability

Protein Stability Prediction Step 3

Step 3

Introduce specific variants to see predicted structural and energy changes

Protein Stability Prediction Step 4

Step 4

Visualize protein mutation stability predictions

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Learn more about Protein Stability Prediction

Resources | Tutorials | FAQs | User Guide

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Resources

Please see our resources below for more information on Lasergene Protein’s protein design software for protein stability prediction.

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Identifying Candidate Variants and Their Effects on Protein Structure

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Hot Spot Scanning Benchmarks in Lasergene Protein

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Structure-guided molecular cloning for improving site-directed mutagenesis and stability in protein design

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How to Screen for Protein Hot Spots in Under 5 Minutes

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Case Study: Structure-Guided Molecular Cloning

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How to perform PCR site-directed mutagenesis using Lasergene’s protein and primer design tools

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Lasergene Protein Overview

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What’s New in Lasergene 16?

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How Can DNASTAR’s Protein Tools Help You?

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Tutorials

Watch one of our videos or check out our user guide to learn more about the protein stability prediction tools available in Lasergene Protein.

Lasergene Protein Overview

This video gives an overview of Lasergene Protein, consisting of Protean 3D, plus the optional services NovaFold, NovaFold Antibody and NovaDock.

Changing Rendering Styles to Highlight Features of Interest

This video demonstrates how Protean 3D makes it easy to highlight features of interest in your structure by changing rendering styles.

Creating Surfaces and Adjusting Lighting on Structures in Protean 3D

In this video, we show you how to create surfaces around your macromolecular structures in Protean 3D. We also show how to adjust lighting to optimize the structure view for presentation.

FAQs

What files types are supported for protein stability predictions?

Protean 3D supports protein structure files from the Protein Data Bank (*.pdb, *.ent, *.pdb.gz, *.ent.gz, *.zip, *.txt), as well as structure files created by Protean 3D (*.structure) or one of our Nova Applications (*.novafold, *.antibody, *.novadock).

How can I predict folding hot spots in my protein structure?

Protean 3D can predict which residues contribute to fold stability more significantly than others using computational alanine scanning or serine scanning. The more destabilizing the alanine/serine variant, the greater the probability that the position and residue…

Protean 3D can predict which residues contribute to fold stability more significantly than others using computational alanine scanning or serine scanning. The more destabilizing the alanine/serine variant, the greater the probability that the position and residue identity is important to the fold.

To predict folding hot spots, choose Modeling > Protein Design > Scan for Hot Spots With > Document. Keep all defaults and choose Run. In most cases, the protein stability prediction results will appear in the Report view in well under a minute.

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How do I run protein stability predictions for mutations on my protein structure?

Within Protean 3D, first select the residues you wish to mutate from the Sequence view . Then, choose Modeling > Protein Design > Create Variant With > Selection. Use the Substitute drop-down menus to select a different amino acid for each position of interest and then click Run. In most cases, protein mutation stability predictions are available in a matter of seconds.

How do I model a mutation from a variant identified in my human genome assembly?

If you are working with reference-guided human assemblies, Lasergene’s SNP to Structure workflow lets you combine genomic sequencing and variant level data with structure files from the RCSB Protein Data Bank (PDB) to model…

If you are working with reference-guided human assemblies, Lasergene’s SNP to Structure workflow lets you combine genomic sequencing and variant level data with structure files from the RCSB Protein Data Bank (PDB) to model point mutations on the protein structure and assess the effect on protein stability. By combining structural bioinformatics with sequencing technologies, this integrated workflow can guide genomic and molecular biology researchers to create structure-based hypotheses and to investigate possibilities not evident by sequences alone.

This workflow requires Lasergene Genomics as well as Lasergene Protein. For detailed guidance on using this workflow, see the Create a reference-guided assembly to use in the SNP to Structure workflow section of the SeqMan NGen User Manual.

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Can I use the protein stability prediction capabilities in Protean 3D to improve my PCR site-directed mutagenesis results?

Yes, the protein mutation stability prediction tools available in our protein design software enable you to introduce specific variants to see how they impact protein structures, including the fold stability and developability of the variant structures. Our…

Yes, the protein mutation stability prediction tools available in our protein design software enable you to introduce specific variants to see how they impact protein structures, including the fold stability and developability of the variant structures. Our PCR site-directed mutagenesis workflow utilizes both protein structure and sequence data to produce the best results and save time over traditional trial-and-error methods. First, utilize Protean 3D to scan for hot spots on your protein structure and test the impact of specific variants on the protein fold stability. Next, use SeqBuilder Pro to introduce variants on the sequence, create a mutated primer, and use the primer to perform in silico cloning.

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