CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins

By Alex S. Holehouse, Rahul K. Das, J. N. Ahad, M. Richardson, Rohit V. Pappu. Biophysical Journal, 2017

452 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5d89fcfd69a6bfe2de0af555ae485c38563d1efd

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In Molecular Biology

Citations in the corpus

Transcription factors interact with RNA to regulate genes (2022, methodology): “13 An approach based on analogous functions in localCIDER (Holehouse et al., 2017) and on a previously applied procedure (Li et al.”
Transcription factors activate genes through the phase separation capacity of their activation domains (2018, methodology): “Net charge per residue for OCT4 was determined by computing the average amino acid charge along the OCT4 amino acid sequence in a 5 amino acid sliding window using the localCIDER package (Holehouse et al., 2017).”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, background): “Weak polyampholites are found in more compact conformations (e.g. the first 100 residues on the protein (cid:2) -synuclein (38)), while negative and positive polyelectrolytes both tend to be found in random coil ensembles (37).”
A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins (2018, methodology): “, 2017) and sequences were analyzed using localCIDER (Holehouse et al., 2017).”
Phase separation of a yeast prion protein promotes cellular fitness (2018, methodology): “pombe was performed using localCIDER (52), IUPred (53), and the SuperFamily database (54).”
A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA (2020, methodology): “The net charge per residue, and the probability of charged residues, were calculated in a sliding window of 10 amino acids using CIDER (Holehouse et al., 2017).”