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protpy

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

v1.5.0 Composition Descriptors (7)

  • cksaap (CKSAAP)

  • cksaagp (CKSAAGP)

  • dde (DDE)

  • asdc (ASDC)

  • distance_pair (DP)

  • natural_vector (NV)

  • atomic_composition (ATC)

v1.5.0 Scales Descriptors (11)

  • z_scales_5 (Z5)

  • vhse (VHSE)

  • atchley_factors (AF)

  • t_scales (T)

  • st_scales (ST)

  • protfp (ProtFP)

  • fasgai (FASGAI)

  • blosum_indices (BLOSUM)

  • ms_whim (MSWHIM)

  • auto_cross_covariance (ACC)

  • physicochemical_distance_transformation (PDT)

v1.5.0 Physicochemical Descriptors (11)

  • charge_fractions (FCR)

  • ncpr (NCPR)

  • kappa (Kappa)

  • sequence_charge_decoration (SCD)

  • charge_density (ChargeDensity)

  • hydrophobicity_profile (HP)

  • hydrophobic_ratio (HydrophobicRatio)

  • half_life (HalfLife)

  • ivywrel_index (IVYWREL)

  • cvp_bias (CvP)

  • flexibility (Flex)

v1.5.0 Complexity Descriptors (3)

  • wootton_federhen_complexity (WF)

  • linguistic_complexity (LC)

  • lempel_ziv_complexity (LZ)

v1.5.0 Signal Descriptors (2)

  • fft_descriptors (FFT)

  • dct_descriptors (DCT)

v1.5.0 Structural Descriptors (10)

  • aggrescan (AGG)

  • uversky_charge_hydropathy (UV)

  • fold_index (FI)

  • disorder_propensity (DP)

  • transmembrane_features (TM)

  • signal_peptide_features (SP)

  • functional_site_counts (FS)

  • plaac (PLAAC)

  • antigenicity_surface (Antigenicity)

  • cysteine_features (Cys)

The v1.5.0 descriptors are added to all_descriptors with descriptor_set="extended" or "all"; see Usage and Descriptor Reference.

Note

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

License

protpy is distributed under the MIT license.

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