Reduction of the Aggregation Propensity of Monoclonal Antibodies


Usage


ANTISOMA is freely available through http://bioinformatics.biol.uoa.gr/ANTISOMA


Submission


You can submit your query either by entering the PDB ID (1) or uploading your own file (2). Using the advanced options (3) you can apply changes to the substitutions table

1: The submission with a PDB ID is completed in 4 steps.

     Step 1: You must insert a valid PDB ID
     Step 2: ID of the light chain as defined in the pdb file
     Step 3: ID of the heavy chain as defined in the pdb file
     Step 4: pH of the solution (between 0 and 14)
     Step 5: ionic strength of the solution (in M)
     Step 6: Press the "Submit" button



2: The submission with an upload of a PDB file is completed in 4 steps.

     Step 1: You must upload a valid pdb file. The file must be in the pdb format and must contain the light and the heavy chain in the same pdb file
     Step 2: ID of the light chain as defined in the pdb file
     Step 3: ID of the heavy chain as defined in the pdb file
     Step 4: pH of the solution (between 0 and 14)
     Step 5: ionic strength of the solution (in M)
     Step 6: Press the "Submit" button



3: Advanced Options.

     Step 1: You can apply changes to the default substitutions table.
     Step 2: Press the save button in order to save your changes
     Step 3: Proceed with the submission ONLY AFTER you have SAVED your changes. Otherwise the changes will be lost and the process will continue with the default substitution table.



Results


 Section 1:

In the first section of the results you can retrieve your personal ID, with which you can have access to your results. Please note that the text output file is maintained in the server for two weeks and can be accessed through the provided link (using your unique id for each submission, e.g. 1466681081). All submissions and results are kept confidential and deleted after one week.
Below is an example of the provided link for the final results file: http://bioinformatics.biol.uoa.gr/ANTISOMA/results/1476890748final_results.txt
Moreover a compressed file with your results is provided using your ID: http://bioinformatics.biol.uoa.gr/ANTISOMA/results/1476890748.tar.gz



 Section 2:


In this section the CDRs (Complementarity Determining Regions) are being predicted, based on Kabat's numbering scheme which is is a widely adopted standard for numbering the residues in an antibody in a consistent manner.

  TABLE CONTENTS:


 Section 3:


In this section the residues that have been chosen for replacement are listed for both the light and the heavy chain. For example: "9:A" means that the 9th Alanine of the chain will be subjected to substitution



 Section 4:


The sequence alignment of the light and the heavy chains of the monoclonal antibody before and after substitutions are presented in this section (in lower case letters are the residues that have been substituted).



 Section 5:


The 'aggregation-prone' regions for the light and the heavy chain are given. The user can see the position of the 'aggregation-prone' regions and the residues before and after substitutions.




Fasta file before and after substiutions


With this option you are able to download the fasta files for your monoclonal antibody in a text file.

Calculate a new model with modeller


With this option the software Modeller (Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints) is used for homology and comparative modelling of protein three-dimensional structures, using the new sequences. Additionally the monoclonal antibody and the new model are visualised in order to compare the aggregation prone regions before and after substitutions.

Section 1:
The left model in this section corresponds to the monoclonal antibody before the substitutions, whereas the right shows the new model created with Modeller. The color code is described below:

Note: The visualization was achieved with JSmol: an open-source Java viewer for chemical structures in three dimensions.


Section 2:
In this section the aggregation prone areas before and after substitutions are compared. The area is calculated with the help of the DSSP algorithm.(Kabsch W, Sander C (1983)) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (12)


Section 3:
The model created can be downloaded as a pdb file and viewed using a Molecular Graphics Program (e.g. PyMol).
Note: The model created can be improved with the use of an energy minimization program.


To download an image file from JSmol:
Right Click on JSmol window and Select File -> Export -> Export PNG Image as shown in the image below