SDPpred

SDPpred identifies specificity-determining positions in protein families from multiple sequence alignments to pinpoint residues responsible for functional specificity between groups.

Key Features:

• Input: Requires a multiple sequence alignment (MSA) of a protein family with sequences categorized into groups based on functional differences in interaction partners.
• Sequence-only analysis: Operates solely on sequence information and does not require structural data.
• SDP identification: Identifies and outputs alignment positions known as specificity determining positions (SDPs) that are likely responsible for functional specificity.
• Comparative group analysis: Detects positions that vary between predefined specificity groups by comparing sequences within each group.

Scientific Applications:

• Protein Family Analysis: Analysis of protein families with members that share biochemical functions but differ in specificity.
• Functional Annotation: Identification of specificity-determining residues to aid annotation of protein functional roles from sequence data alone.
• Drug Design and Biotechnology: Informing design of inhibitors or activators by pinpointing residues that determine substrate or interaction partner specificity.

Methodology:

SDPpred analyzes the provided multiple sequence alignment by comparing sequences within each predefined specificity group (assuming the interaction partner remains constant) to identify alignment positions that vary between groups and are likely responsible for differences in functional interactions.