SAMPDI-3Dv2 webserver

About SAMPDI-3Dv2

SAMPDI-3Dv2 is an updated version of SAMPDI-3D, trained on a larger dataset of mutations in proteins and DNA within protein-DNA complexes. It incorporates an extended feature set and employs a gradient boosting decision tree machine learning algorithm to predict changes in binding free energy caused by mutations in proteins (single amino acid) or DNA (single base-pair).

This method uses two distinct models:

A model trained on single amino acid mutations in proteins and their associated free energy changes, utilizing features derived from protein-DNA complex structures.
A model trained on single base-pair mutations in DNA and their associated free energy changes, leveraging features from protein-DNA complex structures.

The dataset used for model development is available to download. Users can also download the standalone code (available here).

Cite: Rimal, P.; Paul, S.K.; Panday, S.K.; Alexov, E. Genes 2025, 16, 101. https://doi.org/10.3390/genes16010101

ΔΔG — Protein mutation
ΔΔG — DNA mutation

Single mutation
Multiple mutations (batch)

Protein-DNA complex structure

PDB file *

Complex chains *

Job name

Mutation detail

Chain *

Position *

Wildtype *

Mutant *

Protein-DNA complex structure

PDB file *

Complex chains *

Job name

Mutation list file *

Plain text, one mutation per line: CHAIN WTYPE RESID MTYPE — e.g. A W 45 A. View example

Single mutation
Multiple mutations (batch)

Protein-DNA complex structure

PDB file *

Complex chains *

Job name

DNA mutation detail

Chain *

Position *

Wildtype basepair *

Mutant basepair *

Protein-DNA complex structure

PDB file *

Complex chains *

Job name

Mutation list file *

Plain text, one mutation per line: CHAIN WTYPE RESID MTYPE — e.g. C AT 12 GC. View example

Job Submitted

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

Emil Alexov Group

Job Submitted