A user can download a sample protein-DNA complex structure 1AAY.pdb and a protein-mutation-list-file and/or a DNA-mutation-list-file for executing the example. Note to carry out a protein/DNA mutation effect prediction in single mode, one can try a single mutation row information and feed in the single mode form.
SAMPDI-3D predicts the effect of mutation of protein or DNA on protein-DNA binding. The mutation can be in (1). protein or in (2). DNA, each of the two cases has two different modes: Single mode, and multiple mode, both are exemplified below.
User Input for Protein Mutations (1) as shown in Figure 1.
- The Single mode allows the user to submit one single mutation for prediction.
- Users are required to provide a wild-type protein-DNA complex structure by uploading (3) a file in pdb format.
- Details on the single mutation should be provided: (5) residue position, (4) mutated chain, (6) wild type amino acid and (7) mutant amino acid. The residue position must be consistent with the PDB file.
- The Mutation mode option allows the user to submit a list of single mutations to be analyzed in batch.
- Similar to the Single Mutation option, a wild-type protein-DNA complex structure is required and can be input by uploading (8) a file in pdb format.
- The list of single-point mutations must be input (9) by uploading a file containing the mutation information (chain identifier, wild-type residue code, position and mutant residue code). The file format requires one mutation per line (split by space). A sample file is also provided.
Figure 1. Example for protein mutation input form.
User Input for DNA Mutations (2).
- The Single mode allows the user to submit one single mutation for prediction (see Figure 2).
- Users are required to provide a wild-type protein-DNA complex structure by uploading (1) a file in pdb format.
- Details on the single mutation should be provided: (4) residue position, (3) mutated chain, (5) wild type base-pair and (6) mutated base-pair. The residue position must be consistent with the PDB file.
- The Mutation mode option allows the user to submit a list of single mutations to be analyzed in batch(Figure 2).
- Similar to the Single Mutation option, a wild-type protein-DNA complex structure is required and can be input by uploading (2) a file in pdb format.
- The list of single-point mutations must be input (7) by uploading a file containing the mutation information (chain identifier, wild-type base-pair code, position and mutant base-pair code). The file format requires one mutation per line (split by space). A sample file is also provided.
Figure 2. Example for DNA mutation input form.
Results
Figure 3. SAMPSI-3D results for example for protein/DNA mutation.
- The Single mode provides the result at the bottom of the page (Figure 3, left pan).
- The Mutation mode provides the predicted ΔΔG for every single-point mutation will be displayed in a table (Figure 3, right pan).
