Structure-based assignment

Structure-Based Assignment (SBA) is a technique to accelerate the resonance assignment which is a key bottleneck of NMR (Nuclear magnetic resonance) structural biology.^[1] A homologous (similar) protein is used as a template to the target protein in SBA. This template protein provides prior structural information about the target protein and leads to faster resonance assignment . By analogy, in X-ray Crystallography, the molecular replacement technique allows solution of the crystallographic phase problem when a homologous structural model is known, thereby facilitating rapid structure determination.^[2] Some of the SBA algorithms are CAP which is an RNA assignment algorithm which performs an exhaustive search over all permutations,^[3] MARS which is a program for robust automatic backbone assignment ^[4] and Nuclear Vector Replacement (NVR) which is a molecular replacement like approach for SBA of resonances and sparse Nuclear Overhauser Effect (NOE)'s.^[5]^[6]^[7]

References

^ Bartels, Christian; Billeter, Martin; Guentert, Peter; Wuethrich, Kurt (30 April 1996). "Automated sequence-specific NMR assignment of homologous proteins using the program GARANT". Journal of Biomolecular NMR. 7 (3): 207–13. doi:10.1007/BF00202037. PMID 22911044. S2CID 9450778.
^ Rossman, M. G.; Blow, D. M. (1962), "The detection of sub-units within the crystallographic asymmetric unit", Acta Crystallogr. D, 15: 24–31, CiteSeerX 10.1.1.319.3019, doi:10.1107/s0365110x62000067.
^ Al-Hashimi, H. M.; Gorin, A.; Majumdar, A.; Gosser, Y.; Patel, D. J. (2002), "Towards structural genomics of RNA: Rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings", J. Mol. Biol., 318 (3): 637–649, doi:10.1016/s0022-2836(02)00160-2, PMID 12054812.
^ Jung, Y.; Zweckstetter, M. (2004), "Mars - robust automatic backbone assignment of proteins", Journal of Biomolecular NMR, 30 (1): 11–23, doi:10.1023/b:jnmr.0000042954.99056.ad, hdl:11858/00-001M-0000-0012-EC52-9, PMID 15452431, S2CID 3006904.
^ Langmead, C. J.; Yan, A.; Lilien, R.; Wang, L.; Donald, B. R. (2004), "A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments", J. Comp. Bio., 11 (2–3): 277–98, CiteSeerX 10.1.1.15.8054, doi:10.1089/1066527041410436, PMID 15285893.
^ Langmead, C. J.; Donald, B. R. (2004), "An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments", J. Comp. Bio., 29 (2): 111–138, CiteSeerX 10.1.1.630.1110, doi:10.1023/b:jnmr.0000019247.89110.e6, PMID 15014227, S2CID 12443551.
^ Apaydin, M. S.; Catay, B.; Patrick, N.; Donald, B. R. (2010), "NVR-BIP: nuclear vector replacement using binary integer programming for NMR structure-based assignments", The Computer Journal, 54 (January): 708–716, doi:10.1093/comjnl/bxp120, PMC 4287374, PMID 25580019.

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[1] Bartels, Christian; Billeter, Martin; Guentert, Peter; Wuethrich, Kurt (30 April 1996). "Automated sequence-specific NMR assignment of homologous proteins using the program GARANT". Journal of Biomolecular NMR. 7 (3): 207–13. doi:10.1007/BF00202037. PMID 22911044. S2CID 9450778.

[2] Rossman, M. G.; Blow, D. M. (1962), "The detection of sub-units within the crystallographic asymmetric unit", Acta Crystallogr. D, 15: 24–31, CiteSeerX 10.1.1.319.3019, doi:10.1107/s0365110x62000067.

[3] Al-Hashimi, H. M.; Gorin, A.; Majumdar, A.; Gosser, Y.; Patel, D. J. (2002), "Towards structural genomics of RNA: Rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings", J. Mol. Biol., 318 (3): 637–649, doi:10.1016/s0022-2836(02)00160-2, PMID 12054812.

[4] Jung, Y.; Zweckstetter, M. (2004), "Mars - robust automatic backbone assignment of proteins", Journal of Biomolecular NMR, 30 (1): 11–23, doi:10.1023/b:jnmr.0000042954.99056.ad, hdl:11858/00-001M-0000-0012-EC52-9, PMID 15452431, S2CID 3006904.

[5] Langmead, C. J.; Yan, A.; Lilien, R.; Wang, L.; Donald, B. R. (2004), "A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments", J. Comp. Bio., 11 (2–3): 277–98, CiteSeerX 10.1.1.15.8054, doi:10.1089/1066527041410436, PMID 15285893.

[6] Langmead, C. J.; Donald, B. R. (2004), "An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments", J. Comp. Bio., 29 (2): 111–138, CiteSeerX 10.1.1.630.1110, doi:10.1023/b:jnmr.0000019247.89110.e6, PMID 15014227, S2CID 12443551.

[7] Apaydin, M. S.; Catay, B.; Patrick, N.; Donald, B. R. (2010), "NVR-BIP: nuclear vector replacement using binary integer programming for NMR structure-based assignments", The Computer Journal, 54 (January): 708–716, doi:10.1093/comjnl/bxp120, PMC 4287374, PMID 25580019.

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