SAMPDI-3Dv2: Predicting protein-DNA binding free energy change upon mutations

Users can download a sample protein-DNA complex structure file: 1az0.pdb (complexed chains: A, C, D), along with a corresponding protein mutation list file, and/or 3wpd.pdb (complexed chains: A, C) with a DNA mutation list file, to execute the provided examples. For conducting protein or DNA mutation effect predictions in single mode, users can input a single mutation row from the list and use the single mode form for predictions.

SAMPDI-3Dv2 predicts the effect of mutations in either proteins or DNA on protein-DNA binding. Mutations can occur in:

1. Protein, or
2. DNA.

For each case, SAMPDI-3Dv2 supports two operational modes:

1. Single mode: For predicting the effect of a single mutation.
2. Multiple mode: For analyzing the effects of multiple mutations.

Both modes are demonstrated in the examples provided.

SAMPDI-3Dv2 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.

Figure 1. Example for protein mutation input form.

Single Mode

The Single mode allows users to submit a single mutation for prediction by selecting the radio option (3).

• Wild-Type Protein-DNA Complex Structure: Users must upload a wild-type protein-DNA complex structure file in PDB format (5).
• Chain Input: The chains involved in the protein-DNA complex must be present in the PDB file and specified as a string by concatenating chain IDs without spaces (6).
• Job Name: A job name must be provided (7). This job name helps users keep track of multiple calculations performed during their analysis.
• Mutation Details: Users must provide details about the single mutation:
  • (8) Residue position (consistent with the PDB file).
  • (9) Mutated chain ID.
  • (10) Wild-type amino acid.
  • (11) Mutant amino acid.

Once all fields (5–11) are completed, submit the form by clicking Submit (12). Upon successful submission, a result box will appear with a link to the result page (13). Clicking the result link will take you to the results page, where the progress of the job is displayed. Once the job is complete, the results will be shown, with the layout for protein mutation results presented in Figure 2.

Multiple-Mutation/Batch Mode

The Multiple-Mutation/Batch Mode option (4) allows users to analyze a list of single mutations in batch. When this mode is selected, the right-hand form (shown in Figure 1) becomes active, while the left-hand form is disabled.

• Wild-Type Protein-DNA Complex Structure: Similar to Single Mode, users must upload a wild-type protein-DNA complex structure file in PDB format (14).
• Chain Input: The chains involved in the protein-DNA complex must be present in the PDB file and specified as a concatenated string of chain IDs without spaces (15).
• Job Name: A job name must be provided (16) to keep track of multiple calculations.
• Mutation List: Users must upload a file containing the list of single-point mutations (17). The file should follow this format: one mutation per line, with the chain identifier, wild-type residue code, position, and mutant residue code separated by spaces. A sample file is also provided.

After completing all fields (14–17), submit the form by clicking Submit (18). Upon successful submission, a result box will appear with a link to the result page (19). Clicking the result link will take you to the results page, where the progress of the job is displayed. Once the job is complete, the results will be shown, with the layout for protein mutation results presented in Figure 2.

Results for single amino acid mutation in protein.

Figure 2. Example output for protein mutation. (1) column names of the result table and their definitions. (2) result data table, each rows represents a single mutation. (3) The result table can be downloaded as a text file by clicking this link and saving. (4) The files for mutant protein-DNA complex created and used for predictions ca be downloaded from this link.

User Input for DNA Mutations (1) Figure 3.

Figure 3. Example inputs and outputs for DNA mutation.

Single Mode

The Single Mode allows users to submit a single mutation for prediction (see Figure 3, (2)).

• Wild-Type Protein-DNA Complex Structure: Users must upload a wild-type protein-DNA complex structure file in PDB format (4).
• Chain Input: The chains involved in the protein-DNA complex must be present in the PDB file and specified as a string by concatenating chain IDs without spaces (5).
• Job Name: A job name must be provided (6). This job name allows users to keep track of calculations when performing multiple analyses.
• Mutation Details: Users must provide the following details for the single mutation:
  • (7) Residue position (consistent with the PDB file).
  • (8) Mutated chain ID.
  • (9) Wild-type base-pair.
  • (10) Mutated base-pair.

Once all fields (4–10) are completed, users can submit the form by clicking Submit (11). Upon successful submission, a result box will appear, as shown in Figure 3 (12).

Multiple-Mutation/Batch Mode

The Multiple-Mutation/Batch Mode option (3) allows users to analyze a list of single mutations in batch (see Figure 3).

• Wild-Type Protein-DNA Complex Structure: Similar to Single Mode, users must upload a wild-type protein-DNA complex structure file in PDB format (14).
• Chain Input: The chains involved in the protein-DNA complex must be present in the PDB file and specified as a concatenated string of chain IDs without spaces (15).
• Job Name: A job name must be provided (16) to track multiple calculations.
• Mutation List: Users must upload a file containing the list of single-point mutations (17). The file should follow this format: Each line should include the chain identifier, wild-type base-pair code, position, and mutant base-pair code, separated by spaces.
A sample file is also provided for reference.

After completing all fields (14–17), users can submit the form by clicking Submit (18). Upon successful submission, a result box will appear, replacing the area marked as (19) in Figure 3.