Explore the scientific principles, algorithms, and models behind Peptalyzer™. Each resource below explains how we calculate peptide properties such as binding potential, hydropathy, pI, and more.
Stability & Solubility
Peptalyzer™ Polarity Matrix
A proprietary 2D visualization for peptide solubility prediction. It maps hydrophobicity against charge to flag aggregation risks before synthesis.
Aliphatic Index
Originally designed for protein stability, this heuristic helps chemists gauge hydrophobicity and aggregation risks during synthesis.
Secondary Structure Propensity
Chou-Fasman algorithm to map beta-sheet propensity, identifying “difficult sequences” and aggregation hotspots that cause failure during SPPS.
Peptide Charge Distribution
Maps localized charge clustering and 3D topology to identify electrostatic hotspots and surfactant-like risks that global net charge averages fail to detect.
Aromaticity Index
Distinguishes between “standard” and “His-inclusive” aromaticity to predict π–π stacking aggregation risks that standard metrics miss.
Instability Index
Details the Guruprasad method for the Instability Index. Note: This predicts biological in vivo half-life, not chemical shelf-life.
Interaction & Binding
Boman Index
A bio-predictive metric for protein-binding potential. It highlights “sticky” peptides that may complicate purification and analysis.
Hopp-Woods Scale
Highlights hydrophilic segments to identify surface-exposed regions. Used for epitope prediction and troubleshooting synthesis solubility.
Kyte-Doolittle Scale
Provides a residue-by-residue hydrophobicity profile. Useful for identifying hydrophobic cores and assessing aggregation risks in SPPS.
Wimley-White Scale
Calculates the thermodynamic free energy of membrane partitioning. Essential for designing membrane-active peptides and predicting true lipid insertion.
Eisenberg Hydrophobic Moment
Calculates the 3D amphipathicity of folded α-helices using vector mathematics. Essential for identifying membrane-active domains (AMPs) and predicting severe formulation traps like micelles and gels.
Physical Properties & Concentration
Extinction Coefficients
Explains the Pace (ε280) and Anthis & Clore (ε205) methods for calculating accurate concentrations of aromatic and “invisible” peptides.
Isoelectric Point (pI)
A guide comparing industrial pKa scales (IPC 2.0, Bjellqvist, Lehninger) to improve accuracy in peptide design and synthesis.
GRAVY Score
Estimates average hydrophobicity using Kyte-Doolittle values. Essential for predicting solubility, polarity, and membrane association.
Peptide Size Metrics
Explains compact-state volume, equivalent sphere radius, and flexible-chain models for interpreting peptide dimensions and steric behavior in solution.
Peptide Synthesis
SPPS Difficulty Prediction
Predict synthesis risks with Peptalyzer™. Dual-engine logic maps aggregation and kinetic barriers for smarter SPPS planning.
Peptalyzer™ Calculation Framework
Noncanonical Amino Acids
Explains how Peptalyzer™ integrates noncanonical residues across calculations, including analog mapping, partial support, and model limitations.
Terminal Modifications
Explains how N- and C-terminal groups affect mass, charge, pI, UV, and residue-based descriptors in Peptalyzer™.
Z-Scale Peptide Descriptors
A 5D residue descriptor framework that captures multivariate sequence behavior beyond single-value hydropathy scales.