CAMPO

CAMPO analyzes evolutionarily conserved residues (ECRs) within protein families and superfamilies by integrating multiple sequence alignments and three-dimensional protein structures to identify structurally conserved regions (SCRs) and conserved hydrophobic contacts (CHCs).

Key Features:

• Conserved Residue Identification: CAMPO identifies ECRs that are evolutionarily preserved across protein families and superfamilies by mapping conserved amino-acid sites.
• 3D Structural Analysis: The tool examines three-dimensional and superposed protein structures to determine structurally conserved regions (SCRs).
• Multiple Sequence Alignment Integration: CAMPO integrates multiple sequence alignments to facilitate identification of conserved amino-acid sites across homologous sequences.
• Conserved Hydrophobic Contact Computation: It computes residue-to-residue hydrophobic contacts involving only apolar atoms common to all analyzed 3D structures.
• Main-chain Conformation Segment Analysis: CAMPO analyzes segments that maintain similar main-chain conformations across different protein structures.
• Visualization of SCRs, CHCs, and ECRs: The tool visualizes SCRs, CHCs, and ECRs on superposed structures and their multiple alignments for structural interpretation.

Scientific Applications:

• Functional Insights: Identification of ECRs supports interpretation of functional roles for conserved residues within protein families.
• Structural Conservation Analysis: CAMPO enables study of how structural features are preserved across evolutionary related proteins to infer stability and structural constraints.
• Sequence–Structure Mapping: Mapping CHCs and SCRs onto multiple sequence alignments and 3D structures aids interpretation of sequence–structure relationships.

Methodology:

CAMPO analyzes segments with similar main-chain conformations across superposed protein structures, computes residue-to-residue hydrophobic contacts using only apolar atoms common to all analyzed 3D structures, and integrates multiple sequence alignments to map ECRs and identify SCRs and CHCs.