Work

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

Year: 2023

Type: software-paper

Abstract: Conformational heterogeneity is a defining hallmark of intrinsically disordered proteins and protein regions (IDRs). The functions of IDRs and the emergent cellular phenotypes they control are associated with sequence-specific conformational ensembles. Simulations of conformational ensembles that are based on atomistic and coarse-grained models are routinely used to uncover the sequence-specific interactions that may contribute to IDR functions. These simulations are performed either independently or in conjunction with data from experiments. Functionally relevant features of IDRs can span a range of length scales. Extracting these features requires analysis routines that quantify a range of properties. Here, we describe a new analysis suite SOURSOP, an object-oriented and open-source toolkit designed for the analysis of simulated conformational ensembles of IDRs. SOURSOP implements several analysis routines motivated by principles in polymer physics, offering a unique collection of simple-to-use functions to characterize IDR ensembles. As an extendable framework, SOURSOP supports the development and implementation of new analysis routines that can be easily packaged and shared.

Source: Journal of Chemical Theory and Computation

DOI: 10.1021/acs.jctc.3c00190

Authors: Jared M. Lalmansingh, Alex T. Keeley, Kiersten M. Ruff, Rohit V. Pappu, Alex S. Holehouse

Institutions: Washington University in St. Louis, University of Illinois Urbana-Champaign

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green