title: CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins.
abstract: Intrinsically disordered proteins and regions (IDPs) represent a large class of proteins that are defined by conformational heterogeneity and lack of persistent tertiary/secondary structure. IDPs play important roles in a range of biological functions, and their dysregulation is central to numerous diseases, including neurodegeneration and cancer. The conformational ensembles of IDPs are encoded by their amino acid sequences. Here, we present two computational tools that are designed to enable rapid and high-throughput analyses of a wide range of physicochemical properties encoded by IDP sequences. The first, CIDER, is a user-friendly webserver that enables rapid analysis of IDP sequences. The second, localCIDER, is a high-performance software package that enables a wide range of analyses relevant to IDP sequences. In addition to introducing the two packages, we demonstrate the utility of these resources using examples where sequence analysis offers biophysical insights.
authors.affiliation: Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri. Electronic address: alex.holehouse@wustl.edu.
authors.forename: Alex S
authors.initials: AS
authors.lastname: Holehouse
authors.affiliation: Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri.
authors.forename: Rahul K
authors.initials: RK
authors.lastname: Das
authors.affiliation: Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri.
authors.forename: James N
authors.initials: JN
authors.lastname: Ahad
authors.affiliation: Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri.
authors.forename: Mary O G
authors.initials: MO
authors.lastname: Richardson
authors.affiliation: Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri. Electronic address: pappu@wustl.edu.
authors.forename: Rohit V
authors.initials: RV
authors.lastname: Pappu
mesh_terms: D019295:Computational Biology / Q000379:methods*; D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017433:Protein Structure, Secondary
chemical_list: D064267:Intrinsically Disordered Proteins