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

How to Use SAAMBE-MEM

Example input files are provided to help you get started: binding.fasta (also referred as interacting sequence) and mutating.fasta (sample FASTA sequence) and mutation-list-file-format.txt (sample mutation list). Note: lines starting with # in the mutation list file are comments — remove them before submitting.

Single Mutations Mode (I)

• Provide the binding protein sequence (A) — paste sequence (1) or upload a FASTA file (3)
• Provide the mutating protein sequence (B) — paste sequence (2) or upload a FASTA file (4)
• Enter the mutation: residue position (5), wildtype amino acid (6), and mutant amino acid(7)
• Click Submit — results for all mutations appear on the results page.

Multiple Mutations Mode (II)

• Provide the binding protein sequence (A) — paste sequence (1) or upload a FASTA file (3)
• Provide the mutating protein sequence (B) — paste sequence (2) or upload a FASTA file (4)
• Upload a plain text mutation list — one mutation per line: WTYPE POSITION MTYPE (e.g. A 45 G).
• Click Submit — results for all mutations appear on the results page.