SCR_FIND

SCR_FIND identifies structurally conserved regions (SCRs) within protein families and superfamilies by analyzing 3D protein structures and sequence relationships to link structural conservation to functional and evolutionary properties.

Key Features:

• Identification of SCRs: Identifies segments that maintain conserved main-chain conformations across superimposed protein structures.
• Integration with Multiple Sequence Alignments: Integrates 3D structural data with multiple sequence alignments to correlate structural conservation with amino acid sequence variation.
• Visualization Capabilities: Maps SCRs onto superposed 3D structures and corresponding sequence alignments for visual inspection.
• Computation of Hydrophobic Contacts: Computes residue-to-residue hydrophobic contacts involving apolar atoms common across analyzed structures.
• Complementary Tools: Operates alongside CAMPO and CHC_FIND to provide complementary analyses of evolutionarily conserved residues (ECRs) and conserved hydrophobic contacts (CHCs).

Scientific Applications:

• Functional Annotation: Aids prediction of functional sites by highlighting structurally conserved regions likely critical for biological activity.
• Structural Biology Research: Supports studies of protein folding and stability by identifying regions with conserved conformations across species.
• Evolutionary Studies: Facilitates analysis of evolutionary pressures on protein structures by tracing conservation of structural features across homologs.

Methodology:

Analyzes superimposed 3D protein structures alongside homologous sequences and multiple sequence alignments, identifies SCRs based on conserved main-chain conformations, and computes residue-to-residue hydrophobic contacts involving apolar atoms common across analyzed structures.