Coskuner-Weber, OrkidUversky, Vladimir N.2025-02-202025-02-202024978-044321809-5978-044321810-1https://doi.org/10.1016/B978-0-443-21809-5.00015-6https://hdl.handle.net/20.500.12846/1738Intrinsically disordered proteins possess ensembles of conformations and lack stable three-dimensional structures. Phase separation is defined as a phenomenon in which proteins and biomolecules, often including intrinsically disordered proteins, separate from the surrounding solution to form membraneless compartments in the cell. Here, we describe various computational methods and algorithms for studying intrinsically disordered proteins and phase-separated protein states. The methods and algorithms described herein include molecular dynamics and Monte Carlo simulations, machine learning with molecular dynamics, coarse-grained simulations, and bioinformatics. © 2025 Elsevier Inc. All rights reserved.eninfo:eu-repo/semantics/closedAccessBioinformaticsCoarse-grained simulationsIntrinsically disordered proteinsMachine learningMolecular dynamics simulationsMonte Carlo simulationsPhase-separated protein statesBook Part10.1016/B978-0-443-21809-5.00015-63813972-s2.0-85213176908