psico.aggrescanning

Implementation of AGGRESCAN according to Conchillo-Solé et al. 2007 and the corresponding web tool at http://bioinf.uab.es/aap/

Implementation details are tweaked to match the web tool results and may devitate from the paper.

(c) 2022 Thomas Holder (c) 2022 Leukocare AG

License: BSD-2-Clause

Functions

aggrescan1d([selection, key, palette, ...])

Aggrescan (sequence based).

aggrescan1d_scores(seq[, winsize])

Aggrescan reimplementation.

aggrescan3d([selection, palette, minimum, ...])

Aggrescan3d (structure based).

mean(values)

Compute the arithmetic mean

trapezoidal_integration(values)

Trapezoidal integration (midpoint rule)
psico.aggrescanning.aggrescan1d(selection='polymer', key='a4v', palette='white forest', minimum=0, maximum=None, *, var='b', quiet=1, _self=...)[source]

Aggrescan (sequence based).

Arguments

key = a3v | a4v | HSA | NHSA | a4vAHS: Score used for coloring. For the raw aggregation profile, use a4v. For hotspots, use NHSA. {default: a4v}

var = b | q | …: PyMOL property to assign the score to {default: b}

psico.aggrescanning.aggrescan1d_scores(seq: str, winsize: int = 0) → dict[source]

Aggrescan reimplementation.

Equivalent to http://bioinf.uab.es/aggrescan/

Conchillo-Solé et al. AGGRESCAN: a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides. BMC Bioinformatics 8, 65 (2007). https://doi.org/10.1186/1471-2105-8-65

Parameters:

  • seq – Amino acid sequence in single letter code.

  • winsize – Window size, must be odd and larger than 2. A value of 0 will

  • length. (choose a window size based on the sequence)

Returns:

Dictionary with aggregation and hotspot scores.

Dictionary keys:

  • a3vSA: a3v Sequence Average

  • nHS: Number of Hot Spots

  • NnHS: Normalized number of Hot Spots for 100 residues

  • AAT: Area of the Aggregation Profile above the hot-spot Threshold

  • THSA: Total Hot-Spot Area

  • TA: Total Area of the aggregation profile

  • AATr: AAT per residue

  • THSAr: THSA per residue

  • a4vSS: a4v Sequence Sum

  • Na4vSS: Normalized a4vSS for 100 residues

  • a3v: amino-acid aggregation-propensity value

  • a4v: a3v window average

  • HSA: Hot-Spot Area

  • NHSA: Normalized Hot-Spot Area per residue

  • a4vAHS: a4v average in the Hot Spot

psico.aggrescanning.aggrescan3d(selection: str = 'polymer', palette: str = 'white forest', minimum: float = 0, maximum: float = 2, *, ph: float = 7.0, missing: float = 0.0, color_missing: str = 'yellow', state: int = -1, var: str = 'b', quiet: int = 1, exe: str = 'aggrescan', _self=...)[source]

Aggrescan3d (structure based).

psico.aggrescanning.mean(values: list) → float[source]

Compute the arithmetic mean

psico.aggrescanning.trapezoidal_integration(values: list) → float[source]

Trapezoidal integration (midpoint rule)