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• W4367834243 endingPage "2984" @default.
• W4367834243 startingPage "2973" @default.
• W4367834243 abstract "All atom simulations can be used to quantify conformational properties of Intrinsically Disordered Proteins (IDP). However, simulations must satisfy convergence checks to ensure observables computed from simulation are reliable and reproducible. While absolute convergence is purely a theoretical concept requiring infinitely long simulation, a more practical, yet rigorous, approach is to impose Self Consistency Checks (SCCs) to gain confidence in the simulated data. Currently there is no study of SCCs in IDPs, unlike their folded counterparts. In this paper, we introduce different criteria for self-consistency checks for IDPs. Next, we impose these SCCs to critically assess the performance of different simulation protocols using the N terminal domain of HIV Integrase and the linker region of SARS-CoV-2 Nucleoprotein as two model IDPs. All simulation protocols begin with all-atom implicit solvent Monte Carlo (MC) simulation and subsequent clustering of MC generated conformations to create the representative structures of the IDPs. These representative structures serve as the initial structure for subsequent molecular dynamics (MD) runs with explicit solvent. We conclude that generating multiple short (∼3 μs) MD simulation trajectories─all starting from the most representative MC generated conformation─and merging them is the protocol of choice due to (i) its ability to satisfy multiple SCCs, (ii) consistently reproducing experimental data, and (iii) the efficiency of running independent trajectories in parallel by harnessing multiple cores available in modern GPU clusters. Running one long trajectory (greater than 20 μs) can also satisfy the first two criteria but is less desirable due to prohibitive computation time. These findings help resolve the challenge of identifying a usable starting configuration, provide an objective measure of SCC, and establish rigorous criteria to determine the minimum length (for one long simulation) or number of trajectories needed in all-atom simulation of IDPs." @default.
• W4367834243 created "2023-05-04" @default.
• W4367834243 creator A5000531386 @default.
• W4367834243 creator A5031800998 @default.
• W4367834243 creator A5083193340 @default.
• W4367834243 date "2023-05-03" @default.
• W4367834243 modified "2023-09-28" @default.
• W4367834243 title "Critical Assessment of Self-Consistency Checks in the All-Atom Molecular Dynamics Simulation of Intrinsically Disordered Proteins" @default.
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• W4367834243 doi "https://doi.org/10.1021/acs.jctc.2c01140" @default.
• W4367834243 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/37133846" @default.
• W4367834243 hasPublicationYear "2023" @default.
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