NMR-assisted protein structure prediction with MELDxMD
By J. C. Robertson, Roy Nassar, Cong Liu, Emiliano Brini, Ken A. Dill, Alberto Pérez. 2019
20 citations recorded by the source corpus.
We describe the performance of MELD‐accelerated molecular dynamics (MELDxMD) in determining protein structures in the NMR‐data‐assisted category in CASP13. Seeded from web server predictions, MELDxMD was found best in the NMR category, over 17 targets, outperforming the next‐best groups by a factor of ~4 in z‐score. MELDxMD gives ensembles, not single structures; succeeds on a 326‐mer, near the current upper limit for NMR structures; and predicts structures that match experimental residual dipolar couplings even though the only NMR‐derived data used in the simulations was NOE‐based ambiguous atom–atom contacts and backbone dihedrals. MELD can use noisy and ambiguous experimental information to reduce the MD search space. We believe MELDxMD is a promising method for determining protein structures from NMR data.
Subfields: Computational Theory and Mathematics, Molecular Biology, Spectroscopy
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In Computational Theory and Mathematics
- R. Tejero
- Gaetano T. Montelione
- Andriy Kryshtafovych
- T. Ramelot
- Yuanpeng Janet Huang
- Krzysztof Fidelis
- Torsten Schwede
- Maya Topf
In Molecular Biology
- Andriy Kryshtafovych
- Torsten Schwede
- Gaetano T. Montelione
- Krzysztof Fidelis
- John Moult
- Yang Zhang
- Yuanpeng Janet Huang
- Anna Tramontano
In Spectroscopy
- Andriy Kryshtafovych
- Krzysztof Fidelis
- John Moult
- Torsten Schwede
- Gaetano T. Montelione
- Yuanpeng Janet Huang
- Maya Topf
- T. Ramelot
Citations in the corpus
- Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIII (2019, methodology): “Laufer used molecular dynamics with a filtering technique to remove nonconsistent restraints.(39) We hope the encouraging results will lead to larger scale participation in this category in CASP14.”
- Protein storytelling through physics (2020, background): “It adds value in protein structure prediction from sequences (52, 54, 55), native structure determination in conjunction with problematic experimental data (53, 56), ligand binding to proteins (57–59), and finding dynamical routes of conformational change processes (60).”
- AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures (2022, methodology): “Notable among these top-performing NMR-guided prediction groups were methods using NMR-guided MELD (Robertson et al., 2019) and NMR-guided Rosetta (Kuenze and Meiler, 2019) methods.”