Welcome to protpy’s documentation 🧬!

protpy is a Python package for generating a variety of physicochemical, biochemical and structural descriptors for proteins. All descriptors are calculated using sequence-derived or physicochemical features of the constituent amino acids. These descriptors have been widely studied and applied across Bioinformatics applications including protein engineering, SAR (sequence-activity-relationships), predicting protein structure and function, subcellular localization, protein-protein interactions, and drug-target interactions.

The descriptors available in protpy are:

Composition Descriptors (22)

Amino Acid Composition (AAComp)
Dipeptide Composition (DPComp)
Tripeptide Composition (TPComp)
Grand Average of Hydropathy (GRAVY)
Aromaticity
Instability Index
Isoelectric Point
Molecular Weight
Charge Distribution
Hydrophobic/Polar/Charged Composition (HPC)
Secondary Structure Propensity (SSP)
k-mer Composition
Reduced Alphabet Composition
Motif Composition
Amino Acid Pair Composition
Aliphatic Index
Extinction Coefficient
Boman Index
Aggregation Propensity
Hydrophobic Moment
Shannon Entropy
Pseudo Amino Acid Composition (PAAComp)
Amphiphilic Amino Acid Composition (APAAComp)

Autocorrelation Descriptors (3)

Moreaubroto Autocorrelation (MBAuto)
Moran Autocorrelation (MAuto)
Geary Autocorrelation (GAuto)

Conjoint Triad (1)

Conjoint Triad (CTriad)

CTD Descriptors (4)

CTD Composition
CTD Transition
CTD Distribution
CTD Combined

Sequence Order Descriptors (5)

Sequence Order Coupling Number — single (SOCN)
Sequence Order Coupling Number — series
Sequence Order Coupling Number — all matrices
Quasi Sequence Order (QSO)
Quasi Sequence Order — all matrices

Note

A demo of the software is available on Colab and a Medium article covering the background of protpy is available on Medium.