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 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.

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 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.

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 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.