Question: What is the purpose of the SAMPDI-3D server?
Answer:
SAMPDI-3D is a Machine learning based method for predicting the effect of mutation in protein or DNA on the binding affinity of protein-DNA complex. It is a very fast and currently outperformes all state-of-the-art methods, which suites best for the genome level protein-DNA interaction investigations.
Question: What is methodology used in the SAMPDI-3D server?
Answer:
SAMPDI-3D uses a gradient boosting decision tree machine learning algorithm with features as physicochemical properties, structure of mutation site and protein-DNA interactions to predict the change of binding free energy.
Question: What kind of mutations effect can be predicted using the SAMPDI-3D?
Answer:
The SAMPDI-3D webserver is designed to predict effect one of the following two types of mutations at a time.
- Protein mutation
- DNA mutation
Question: What inputs are required to predict the effect of protein mutation(s) using SAMPDI-3D?
Answer:
To predict the effect of protein mutation(s) using SAMPDI-3D, user required to provide following inputs in single and batch(multiple) modes.
Single mode
- A protein-DNA complex structure in PDB v3.0 file format.
- Mutation information: chain in which the residue to be mutated exists, its residue id in structure, name of the residue and the mutated residue.
Multiple/batch mode
- A protein-DNA complex structure in PDB v3.0 file format.
- Mutations information: a text (.txt) file containng one mutation per line. The mutation chain in which the residue to be mutated exists, wildtype residue code (single letter code), its residue id in structure, mutated residue (single letter code).
Question: What inputs are required to predict the effect of DNA mutation(s) using SAMPDI-3D??
Answer:
To predict the effect of DNA mutation(s) using SAMPDI-3D, user required to provide following inputs in single and batch(multiple) modes.
Single mode
- A protein-DNA complex structure in PDB v3.0 file format.
- Mutation information: chain in which the forward strand base to be mutated exists, residue ids of forward & backward strand base-pairs in structure(pair of single letter codes), name of the residue and the mutated base-pair.
Multiple/batch mode
- A protein-DNA complex structure in PDB v3.0 file format.
- Mutations information: a text (.txt) file containng one mutation per line. The mutation chain in which the forward strand base to be mutated exists, wildtype base-pairs (pair of single letter code), its residue id in structure, mutated base-pair.
Question: How much time SAMPDI-3D takes to predict the effect of single mutation?
Answer:
Most often our SAMPDI-3D webserver predicts effect of single mutation within a few seconds.
Question: How does SAMPDI-3D treats non-standard amino acids and/or small molecules or ions if any are present in the complex structure?
Answer:
SAMPDI-3D will ignore non-standard amino acids or small molecules, the inclusion of them in the structure will not affect the prediction result.
Question: What shall I do if i find some problem using SAMPDI-3D or apperently I discover a bug?
Answer:
In any such case kindly contact us at
delphi@g.clemson.edu. We will try our best to resolve your query as soon as possible.
