Demo
In this tutorial, we will generate CDRs for the antigen of SARS-Cov-2 spike protein using PDB ID: 7BZ5.
| Step | Method |
|---|---|
| Step1 |
To submit the job, go to "Job Submission" page. |
| Step2 |
Enter your job name at “Name” field and your email at "Email" field. (Optional) If you want to secure your job, enter the password at "Password" field. The result file will be secured by 7z format with the password. |
| Step3 |
Enter PDB ID to optimize antibody. The PDB should contain both antibody and antigen structure. Here we will enter “7bz5”. (Optional) If you want to use a custom PDB file, upload your PDB file using browse button at “Pdb file” field. |
| Step4 |
Set your CDR optimization configurations using “Antibody chains”, “Antigen chains”, “Design chain”, “CDR type”, and “CDR sequence” field. - Antibody chains: antibody chains to be considered. Enter the chains with ‘,’ separator. CASE-SENSITIVE! - Antigen chains: antigen chains to be considered. Enter the chains with ‘,’ separator. CASE-SENSITIVE! - Design chain: the antibody chain to be designed. Enter one antibody chain. - CDR type: Enter one CDR type to be designed in the antibody. “H1”, “H2”, “H3”, “L1”, “L2”, and “L3” are allowed. - CDR sequence: enter CDR sequence to be designed. In this demo, we will used the values below. - Antibody chains: H,L - Antigen chains: A - Design chain: H - CDR type: H3 - CDR sequence: EAYGMDV |
| Step5 |
Set antibody structure modeling configurations using “Sample number”, “Relax number”. - Sample number: how many antibody samples to be generated. Max=50 - Relax number: how may times the generated antibody structure will be optimized using openMM. Max=10 Here we will use the values below. - Sample number: 10 - Relax number: 5 |
| Step6 |
Click the "Send" button and check the job has been submitted at "Queue" page. |
Queue Page
Chek the submitted job at "Queue" page.
| Category | Contents |
|---|---|
| Job ID |
ID number of the submitted job. |
| Status |
Not starged yet: The job is submited to the server but not started yet. If the job is not started within few minutes, please check the input information again or contact to the server manager (jjs092@kaist.ac.kr). Job is running: The job is successfully running on the server. Job is finished: The job is finished and you can download the result file. Error occurred: The job is stopped by error. Please check the input information whether it is entered correctly. For more information on the error, we provide "error_log.txt" file, the error log of the job. You can download the log file via download link of the queue page. |
| Job Name |
The name of job submitted. |
| Submitted Time |
Submitted time of the job. |
| Download Link |
If the job has finished successfully, then the Download link of the result will appear. If the job has occured an error, then an "Error" link will be appread. The "Error" link contains detailed information about the error. |
Result Files
Inside the download file, you will find below files and folder.
| Category | Contents |
|---|---|
| {pdb_id}_{chain_id}_ {CDR_type}_{sample#}_openmm.pdb |
The relaxed full-atom model built with the predicted CDR C alpha coordinates and samples sequences. |
| {pdb_id}_{chain_id}_ {CDR_type}_sequence_samples.fasta |
The file of generated antibody chain sequences that were sampled from the predicted probability distribution. |
| {pdb_id}_{chain_id}_ {CDR_type}_{sample#}_best_IA.pdb |
The best binding energy structure calculated by Rosetta InterfaceAnalyzer through the relaxation. |
| {pdb_id}_*_energy_scores.xlsx |
Calculated binding energies of the generated samples.. |