PepStr

PepStr predicts the tertiary structures of small bioactive peptides (7–25 residues) with emphasis on identifying β-turns and secondary structure elements.

Key Features:

• Peptide length range: Predicts tertiary structures for peptides of 7–25 residues.
• β-turn prevalence analysis: Analysis of 77 biologically active peptides showed 58 contained at least one β-turn, with 34.9% of residues in β-turns versus 32.3% helical and 6.9% beta-sheet residues.
• PSIPRED integration: Incorporates PSIPRED to provide regular secondary structure predictions including helices, beta-strands, and coils.
• BetaTurns prediction: Uses BetaTurns to predict β-turn types.
• Model I: Builds an all-extended conformation with phi and psi angles set to 180 degrees for all residues.
• Model II: Incorporates regular secondary structure information from PSIPRED, including helices, beta-strands, and coils.
• Model III: Utilizes both regular secondary structures and β-turn types predicted by BetaTurns.
• Model IV: Extends Model III by assigning side-chain angles using the Dunbrack backbone-dependent rotamer library.
• Energy refinement: Refines models using the AMBER package and energy minimization, optimizing structural accuracy measured by C(alpha) root mean square deviation (rmsd), with inclusion of β-turns reducing rmsd before and after minimization.

Scientific Applications:

• Peptide structural analysis: Prediction and analysis of three-dimensional structures of small bioactive peptides to inform studies of structure–function relationships.
• Secondary structure investigation: Quantitative assessment of β-turn, helix, and beta-sheet content in bioactive peptides.
• Peptide therapeutics: Support for peptide-based drug design and therapeutic development through structural modeling and refinement.

Methodology:

Integrates PSIPRED regular secondary structure predictions and BetaTurns β-turn type predictions; constructs four models (Model I: all residues extended with phi/psi = 180 degrees; Model II: includes PSIPRED secondary structures; Model III: adds BetaTurns β-turn types; Model IV: assigns side-chain angles from the Dunbrack backbone-dependent rotamer library); refines models with the AMBER package and energy minimization and evaluates structural accuracy by C(alpha) rmsd.