Antibody discovery, engineering, and characterization work involves a great deal of uncertainty about the materials at hand. There are important theoretical calculations necessary for analysis as well as variations of molecules that need to be explored. Scientists want to consider and run calculations several different ways based on variations/modifications they are working with for analysis and inclusion in a notebook.
In the case of a structure format not being recognized, e.g. some scFv diabody, it will not be properly classified and the calculations will be wrong. Providing the ability to reclassify and recalculate molecular physical properties is key for assisting with scenarios such as "What if this S-S bond formed or didn’t?"
Using the built-in Molecular Physical Property Calculator
, you can view the persisted calculations to make your input conditions and calculation type clearer and select alternative conditions and calculations for your entity.
We currently calculate average mass, pI (isoelectric point), and 𝜺 (extinction coefficient) from the sequence, molecular stoichiometry, number of free Cysteine and disulfide bonds. While including stoichiometry, free Cys vs S-S, these inputs include sequence scope/type.
View Physical Property Calculator
From the grid of Molecules
, select the Molecule of interest. Click the Physical Property Calculator
In the Calculation Inputs
panel, you'll enter the values to use in the calculation:
- Num S-S
- Num Cys
- Sequence ranges for each component sequences. For each, enter:
- Use Range: Enter the start and end positions. You can click View this sequence to open the entire annotated sequence in a new tab for reference.
- Analysis Mode. Select from:
- Alkylated Cysteine (only available in "Reduced" mode). If available, select the desired value.
- Pyro-glu: Check the box for "Cyclize Gln (Q) if at the N-terminus"
- PNGase: Chec the box for "Asn (N) -> Asp (D) at N-link sites"
to see the calculations based on your inputs.
When you click Calculate
, the right hand panel of Properties
will be populated. You'll see both what the Classifier Generated
value is (if any) and the Simulated
value using the inputs you entered.
Calculations are provided for:
- Average Mass
- Monoisotopic Mass
- Organic Average Mass
- pI - Isoelectric Point calculated by different methods:
- Patrickios (simple)
- Sillero (abridged)
- Chemical Formula
- Extinction Coefficient - ε
- Percent Extinction Coefficient
- Sequence Length
- Amino Acid (AA) composition
To export the resulting calculated properties, click Export Data
The exported Excel file includes both the calculated properties and the inputs you used to determine them. For example, the export of the above-pictured M-17 calculation would look like this: