SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins

JM Lalmansingh and AT Keeley and KM Ruff and RV Pappu and AS Holehouse, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 19, 5609-5620 (2023).

DOI: 10.1021/acs.jctc.3c00190

Conformational heterogeneity is a defining hallmark ofintrinsicallydisordered proteins and protein regions (IDRs). The functions of IDRsand the emergent cellular phenotypes they control are associated withsequence-specific conformational ensembles. Simulations of conformationalensembles that are based on atomistic and coarse- grained models areroutinely used to uncover the sequence-specific interactions thatmay contribute to IDR functions. These simulations are performed eitherindependently or in conjunction with data from experiments. Functionallyrelevant features of IDRs can span a range of length scales. Extractingthese features requires analysis routines that quantify a range ofproperties. Here, we describe a new analysis suite simulation analysisof unfolded regions of proteins (SOURSOP), an object- oriented andopen-source toolkit designed for the analysis of simulated conformationalensembles of IDRs. SOURSOP implements several analysis routines motivatedby principles in polymer physics, offering a unique collection ofsimple-to-use functions to characterize IDR ensembles. As an extendableframework, SOURSOP supports the development and implementation ofnew analysis routines that can be easily packaged and shared.

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