Introducing idpr: A Package for Profiling and Analyzing Intrinsically Disordered Proteins in R.
William Michael McFadden,Judith L. Yanowitz Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA
Abstract
Intrinsically Disordered Proteins (IDPs) are proteins or protein-domains that do not have a single native structure but rather are dynamic peptides that can adopt multiple conformations. The field of “unstructured biology” has gained prominence over the last few decades as it has become apparent that proteins experiencing intrinsic disorder comprise substantial portions of proteomes. IDPs have been implicated in many fascinating biological phenomena such as liquid-liquid phase separation, prion diseases, the evolution of multicellularity, and even the origin of life. The emergence of IDPs as a field of research is the result of many computational biology and bioinformatic studies that have identified unique characteristics and trends among IDPs and IDRs (intrinsically disordered regions). The package ‘idpr’, short for “Intrinsically Disordered Proteins in R”, implements several functions that can identify characteristics associated with IDPs in a protein of interest. This includes residue composition, charge-hydropathy relationships, and predictions of intrinsic disorder. Additionally, ‘idpr’ integrates well with other R packages by accepting various input formats and includes tools to supplement IDP-based sequence analysis. Results are returned as ggplot visualizations or manageable datasets to balance ease-of-use with customization. Overall, ‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins within R, facilitating the analysis of these important, yet uncharacterized, proteins.
Keywords: intrinsically disordered proteins,structure prediction