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.{{cite journal|last=Bartels|first=Christian|author2=Billeter, Martin|author3=Guentert, Peter|author4=Wuethrich, Kurt|title=Automated sequence-specific NMR assignment of homologous proteins using the program GARANT|journal=Journal of Biomolecular NMR|date=30 April 1996|volume=7|issue=3|pages=207–13|doi=10.1007/BF00202037|pmid=22911044|s2cid=9450778 }} 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.{{citation
| last1 = Rossman| first1 = M. G.
| last2 = Blow| first2 = D. M.
| journal = Acta Crystallogr. D
| pages = 24–31
| title =The detection of sub-units within the crystallographic asymmetric unit
| volume = 15
| date = 1962
| doi=10.1107/s0365110x62000067
| citeseerx = 10.1.1.319.3019
}}. Some of the SBA algorithms
are CAP which is an RNA assignment algorithm which performs an exhaustive search over
all permutations,{{citation
| last1 = Al-Hashimi| first1 = H. M.
| last2 = Gorin| first2 = A.
| last3 = Majumdar| first3 = A.
| last4 = Gosser| first4 = Y.
| last5 = Patel| first5 = D. J.
| issue=3
| journal = J. Mol. Biol.
| pages = 637–649
| title =Towards structural genomics of RNA: Rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings
| volume=318
| date = 2002| doi=10.1016/s0022-2836(02)00160-2| pmid=12054812
}}. MARS which is a program for robust automatic backbone assignment {{citation
| last1 = Jung| first1 = Y.
| last2 = Zweckstetter| first2 = M.
| issue = 1
| journal = Journal of Biomolecular NMR
| pages = 11–23
| title =Mars - robust automatic backbone assignment of proteins
| volume = 30
| date = 2004
| doi=10.1023/b:jnmr.0000042954.99056.ad
| pmid = 15452431
| hdl = 11858/00-001M-0000-0012-EC52-9
| s2cid = 3006904
| hdl-access = free
}}. and Nuclear Vector Replacement (NVR) which is a molecular replacement like approach for SBA of resonances and
sparse Nuclear Overhauser Effect (NOE)'s.{{citation
| last1 = Langmead| first1 = C. J.
| last2= Yan| first2= A.
| last3= Lilien| first3= R.
| last4= Wang| first4= L.
| last5 = Donald | first5 = B. R.
| issue = 2–3
| journal = J. Comp. Bio.
| pages = 277–98
| title =A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments
| volume = 11
| date = 2004| doi=10.1089/1066527041410436
| pmid = 15285893
| citeseerx = 10.1.1.15.8054
}}.{{citation
| last1 = Langmead| first1 = C. J.
| last2 = Donald | first2 = B. R.
| issue = 2
| journal = J. Comp. Bio.
| pages = 111–138
| title =An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments
| volume = 29
| date = 2004
| doi=10.1023/b:jnmr.0000019247.89110.e6
| pmid = 15014227
| citeseerx = 10.1.1.630.1110
| s2cid = 12443551
}}.{{citation
| last1 = Apaydin | first1 = M. S.
| last2 = Catay | first2 = B.
| last3 = Patrick | first3 = N.
| last4 = Donald | first4 = B. R.
| doi= 10.1093/comjnl/bxp120
| pmid = 25580019
| issue = January
| pages = 708–716
| journal = The Computer Journal
| title = NVR-BIP: nuclear vector replacement using binary integer programming for NMR structure-based assignments
| date =2010 | volume=54| pmc = 4287374}}.