SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets

Abstract

The emergence of high-throughput experiments and high-resolution computational predictions has led to an explosion in the quality and volume of protein sequence annotations at proteomic scales. Unfortunately, integrating and analyzing complex sequence annotations remains logistically challenging. Here we present SHEPHARD, a software package that makes large-scale integrative protein bioinformatics trivial. SHEPHARD is provided as a stand-alone package and with a pre-compiled set of human annotations in a Google Colab notebook.

Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease

“…The protein sequence analysis was conducted using SHEPHARD, a Python-based framework designed for integrating and analyzing large-scale amino acid sequence properties 124 . IDRs were predicted and annotated using metapredict (V2) 125 .…”

“…Protein abundance analyses (Fig. S7–11) were performed using SHEPHARD 124 and sparrow (https://github.com/idptools/sparrow). Mass spectrometry data were obtained for humans 128 , X. laevis 129 , A. thaliana 130 , E. coli 131 , S. pombe 132 , and S. cerevisiae 133 .…”

Direct prediction of intrinsically disordered protein conformational properties from sequence

“…Proteome-wide bioinformatic analyses were performed using SPAR-ROW (https://github.com/idptools/sparrow) and SHEPHARD 96 . SPARROW is an in-development Python package for calculating IDR sequence properties and SHEPHARD is a hierarchical analysis framework for annotating and analyzing large sets of protein sequences.…”

Direct prediction of intrinsically disordered protein conformational properties from sequence

“…Proteome-wide bioinformatics was performed using SPARROW (https://github.com/idptools/sparrow) and SHEPHARD 66 . SPARROW is an in-development Python package for calculating IDR sequence properties, while SHEPHARD is a hierarchical analysis framework for annotating and analyzing large sets of protein sequences.…”

“…4 and Fig. 5 are shared as SHEPHARD-compliant datafiles, and we encourage other groups to explore these predictions in the context of other protein annotations using SHEPHARD and the set of precomputed annotations provided therein 66 . All other data and code used for sequence analysis, training weights, bioinformatic data, the SPARROW implementation, and the Google Colab notebook are linked from this manuscript's main GitHub directory: https://github.com/holehouse-lab/supportingdata/tree/master/2023/ALBATROSS_2023…”