A Benchmark Study of Protein–Fragment Complex Structure Calculations with NMR2
Abstract
:1. Introduction
2. Results
2.1. NMR2 Performances with Exact Distances
2.2. Conditions on the Binding Site Topology
2.3. Impact of the Distance Restraints Tolerance and Protein Partial Assignment on the NMR2 Convergence
2.4. Distance Restraints Network Topology Is Critical for a Successful NMR2 Structure Calculation
2.5. Computational Time
3. Discussion
4. Material and Methods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Distance Restraints Tolerance | Success Rate | rmsd (Å) | TFC | Success: rl rw | Fail: rl rw |
---|---|---|---|---|---|
0% | 95% | 0.88 ± 0.42 | 2.56 ± 3.00 | 1.55 ± 0.58 | 0.98 ± 0.33 |
0.87 ± 0.43 * | 3.68 ± 3.50 * | 0.91 ± 0.32 | 0.84 ± 0.16 | ||
10% | 57% | 1.05 ± 0.53 | 1.58 ± 1.99 | 1.63 ± 0.58 | 1.16 ± 0.41 |
0.74 ± 0.29 * | 2.16 ± 1.93 * | 0.95 ± 0.33 | 0.78 ± 0.21 | ||
20% | 46% | 0.96 ± 0.27 | 0.98 ± 2.85 | 1.79 ± 0.44 | 1.25 ± 0.58 |
0.97 ± 0.32 * | 1.50 ± 3.48 * | 1.00 ± 0.26 | 0.82 ± 0.33 | ||
10% (PA) | 92% | 0.85 ± 0.34 | 3.20 ± 3.80 | 1.57 ± 0.56 | 0.88 ± 0.29 |
0.76 ± 0.26 * | 4.51 ± 4.50 * | 0.94 ± 0.28 | 0.56 ± 0.50 | ||
20% (PA) | 70% | 1.09 ± 0.51 | 2.29 ± 3.73 | 1.74 ± 0.49 | 0.99 ± 0.39 |
0.93 ± 0.29 * | 3.63 ± 4.45 * | 0.99 ± 0.26 | 0.72 ± 0.34 |
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Torres, F.; Stadler, G.; Kwiatkowski, W.; Orts, J. A Benchmark Study of Protein–Fragment Complex Structure Calculations with NMR2. Int. J. Mol. Sci. 2023, 24, 14329. https://doi.org/10.3390/ijms241814329
Torres F, Stadler G, Kwiatkowski W, Orts J. A Benchmark Study of Protein–Fragment Complex Structure Calculations with NMR2. International Journal of Molecular Sciences. 2023; 24(18):14329. https://doi.org/10.3390/ijms241814329
Chicago/Turabian StyleTorres, Felix, Gabriela Stadler, Witek Kwiatkowski, and Julien Orts. 2023. "A Benchmark Study of Protein–Fragment Complex Structure Calculations with NMR2" International Journal of Molecular Sciences 24, no. 18: 14329. https://doi.org/10.3390/ijms241814329