Protein FASTA
Copyright 2026 Witold Wolski

This product includes modified source-derived behavior from FDR Benchmark,
Copyright 2026 Functional Genomics Center Zurich, revision
bbf582e382833cf8bdc439e69edb287842293b02, under the Apache License 2.0.

FDR Benchmark in turn records the following attributions:

- PGATK, https://github.com/bigbio/pgatk, reviewed revision cdedf9057e7e.
  Its DecoyPYrat reverse/switch and collision workflow informed the decoy
  generation implementation.
- FDRBench, https://github.com/Noble-Lab/FDRBench, reviewed revision
  5deac96dfa0e. Its entrapment-generation behavior informed the entrapment
  generation implementation.

The original projects and associated publications retain their respective
copyrights and attribution. See LICENSES/Apache-2.0.txt for the applicable
third-party license.

The dipeptide instability weight values in
src/protein_fasta/analytics/peptide_properties.py are taken from Biopython
1.86, Bio/SeqUtils/ProtParamData.py, Copyright (c) 1999-2024 The Biopython
Contributors, under the BSD 3-Clause License (two entries changed to the
values of the R package Peptides). See LICENSES/BSD-3-Clause-Biopython.txt.

The reversed-phase retention coefficients and length-corrected retention
model in the same file are taken from Pyteomics 4.7.5, pyteomics/achrom.py
(RCs_zubarev, calculate_RT), under the Apache License 2.0; see
LICENSES/Apache-2.0.txt. Pyteomics: Goloborodko et al., J Am Soc Mass Spectrom
2013, 24(2):301-304; Levitsky et al., J Proteome Res 2019, 18(2):709-714. The
coefficients: Goloborodko et al., Rapid Commun Mass Spectrom 2010,
24(4):454-462.
