On the homepage of 3dpredict/Ab you can submit a new job by clicking on the "Start from Structures Icon"
This will open up a job submission dialog allowing you to provide your own structures as input and subsequently submit them for calculation. Once you clicked on Start from Structures you'll see the following dialog
Job submission dialog
Each section of the dialog will be explained hereafter using the orange indicators of the dialog above.
A: Input section
In the input section you can either choose to upload one or multiple files or directly paste sequences.
File Input
In this dialog you can drop one or multiple files containing 3d antibody structures. Supported file formats are: PDB, mmCIF, MOE and their corresponding gzipped formats. You can get started with a sample file here:
B: Job Name
Be creative and give an informative job name here, it should be short & clear. This is the identifier allowing to find your results at later stages as well, so it should be easily recognizeable by you. For instance your project name / identifier & stage or campaign name.
C: Job Description
Here you can add more details in which context you run the calculation & why with these parameters like at lower pH levels etc.
D: Annotation Scheme
Here you have the choice on how to annotate & number the output model and residue numbers. 5 different choices are available among the most commonly used antibody numbering schemes.
The Annotation scheme has an impact on two things in the output of the predictions, the aminoacid sequence numbering in the tables & the structure and on the defintions of CDR ranges on the sequence.
E: pH
By default you'll run the property calculation at pH 7.4, but you can change to any valid pH here. Note, that 3dpredict/Ab will run an ensemble of property calculations on conformations around the pH of your choice. For pH 7.4 for instance a pH range from 6.4 to 8.4 is sampled with 100 conformations in total to extract the final descriptors and 95% confidence intervals.
F: Salt type
If you want to change the salt used for the simulation from NaCl to KCl you can do that here
G: Salt concentration
Here you can adapt the salt concentration used for the simulation to match your real life conditions
H: Runtime & Cost
Once you uploaded your structures they get analyzed and an estimated cost and runtime projection will be shown here. This projection depends on the size of the submitted structure. This allows you to have an approximative estimate of how long your calculation will run and how many credits will be consumed.
For more information on credits you can refer to the credits section of this documentation