CompBio» SAAMBE-MEM webserver

About SAAMBE-MEM

SAAMBE-MEM is a sequence based machine learning method for predicing the binding free energy change in membrane protein-protein complexes upon mutation. This method uses experimental binding affinities due to mutation in membrane proteins compiled in MPAD database. The present method uses evolutionary features of the involved protein sequences, and an XGBoost regression model is trained to make the predictions. The cleaned version of MPAD used in this work is available here.

Please see the publication for greater details and cite to acknowledge the use of SAAMBE-MEM in your work:

Rimal, P.; Panday, S.K.; Xu, W.; Peng, Y.; Alexov, E. SAAMBE-MEM: A Sequence-Based Method for Predicting Binding Free Energy Change upon Mutation in Membrane Protein-Protein Complexes. Bioinformatics 2024 https://doi.org/10.1093/bioinformatics/btae544

Single mutation mode

Binding Protein sequence

Paste protein sequence in the text area

Mutating Protein sequence

Paste protein sequence in the text area

Choose the binding protein .fasta file

Choose the mutating protein .fasta file

Mutation detail (required for both cases: sequence or file)

Position:

Wildtype Amino acid:

Mutated Amino acid:

Multiple mutation mode

Binding Protein sequence

Paste protein sequence in the text area

Mutating Protein sequence

Paste protein sequence in the text area

Choose the binding protein .fasta file

Choose the mutating protein .fasta file

Mutation list file(required for both cases: sequence and file)

Upload a plain text file with one mutation per line, click here to view an example for reference

Mutations list (allowed only .txt)

SAAMBE-MEM: A Sequence-Based Method for Predicting Binding Free Energy Change upon Mutation in Membrane Protein-Protein Complexes

Professor Emil Alexov Group