| Autor: |
Masetti M; Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Università di Bologna, Bologna, Italy., Bernetti M; Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy., Cavalli A; Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Università di Bologna, Bologna, Italy. andrea.cavalli@iit.it.; Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy. andrea.cavalli@iit.it. |
| Jazyk: |
angličtina |
| Zdroj: |
Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2020; Vol. 2141, pp. 391-411. |
| DOI: |
10.1007/978-1-0716-0524-0_19 |
| Abstrakt: |
Molecular dynamics simulations represent a powerful tool to gain insights into structural and dynamical features of biomolecular systems. Nevertheless, their recognized limitation in terms of achievable timescales becomes particularly severe when dealing with slow processes. In such cases, the employment of enhanced sampling methods, which allow accelerating the characterization of rare events in a timeframe consistent with conventional computational resources, results as crucial. In particular, such advanced techniques have proven highly valuable in the context of protein folding and, specifically, to explore the conformational ensemble spanned by intrinsically disordered proteins (IDPs). Here, we describe how to set up molecular dynamics simulations with one of these enhanced sampling approaches (namely, Parallel Tempering Metadynamics in the Well-Tempered Ensemble) using the N TAIL peptide as a test case. |
| Databáze: |
MEDLINE |
| Externí odkaz: |
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