About EmCAST

Welcome to the Empirical C-Alpha Stability Tool (EmCAST).

EmCAST uses the positions of alpha carbons within a protein's backbone to analyze structure. The software can currently be used to visualize the four residue dihedral angle (τ) preferences of a sequence or structure. Stability changes from mutations at solvent accessible sites on the protein can be rapidly predicted.

This software is freely available for academic users.

Citation

Please include the following citation when using EmCAST in your published research:

High-Accuracy Prediction of Stabilizing Surface Mutations to the Three-Helix Bundle, UBA(1), with EmCAST

Michael T. Rothfuss, Dustin C. Becht, Baisen Zeng, Levi J. McClelland, Cindee Yates-Hansen, and Bruce E. Bowler

Journal of the American Chemical Society 2023 145 (42), 22979-22992

DOI: 10.1021/jacs.3c04966

 
 
 
 
 

Protein Sequences and Conformers

Protein sequences can be entered manually here or imported directly from a PDB file in the Import PDB page. If you only have a partial structure, or your structure has unresolved segments, it is recommended to enter the full sequence here before importing a PDB file.

Only the 20 standard amino acids are supported at this time.

Select a Sequence


Offset specifies the residue number your sequence starts at.



Select a Conformer

The above Tetrad Heatmap will update to represent the tetrad dihedral angles found in the selected conformer with black/white dots. If the selected conformer contains point mutations, the affected tetrads will be highlighted in red and the associated sections of the heatmap will be updated. Once a conformer is selected, mutations can be analyzed below.


Mutations

Mutations are scored in the context of a seven residue fragment containing the mutation site at the center. If the mutation site does not interact with any residues outside this interaction window (ie: at solvent accessible sites), the prediction should be reliable. Only aqueous conditions near neutral pH are supported. Solvent Accessible Surface Area (SASA) is provided as a percentage to help identify viable mutation sites. Statistics on the number of protein fragments used in the calculation are also included. Multiple fragment datasets are used in each calculation. The "Minimum Samples" statistic reflects the weakest link in the calculation; calculations with less than 20 samples are unreliable. Positive values for ΔΔG are stabilizing.

Multiple output formats are available. In the "Table" format, mutations that are destabilizing by at least 0.2 kcal/mol are colored red and mutations that are stabilizing by at least 0.2 kcal/mol are colored green. The "Heatmap" format shows a grid of all possible mutations colored by stability; The X-axis lists the WT sequence, the Y-axis lists potential mutations. Hovering the mouse over a cell in the grid will reveal the data associated with the mutation. Stabilizing mutations are colored yellow to red, destabilizing mutations are colored cyan to blue. Grey cells do not have data associated with them; dark grey cells are the WT residue, light grey cells were excluded by the calculation parameters. Black cells have insufficient data to perform the calculation.

Calculation Parameters:

Protein Structures

Multiple structures may be associated with a single sequence to compare different conformers or variants during analysis.

If you only have a partial structure, or if your structure has unresolved segments, you should define the full sequence in the Analysis page before importing a structure.

Load a PDB

Enter an RCSB PDB code or upload a file


End User License Agreement


Activation

Passwords are securely transmitted and stored using SHA-2 cryptographic hash functions.

Account Registration

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Account Registration

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