BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB
 
RESCUE: An artificial neural network tool for the NMR spectral assignment of proteins
J.L. Pons and M.A. Delsuc

Centre de Biochimie Structurale UMR 9955, U 414, UMI,
15 avenue Charles Flahault, F-3400 Montpellier,
France







Abstract:  The assignment of the 1H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies.  We present here an assignment tool based on the artificial neural network technology, which determines the type of amino acid from the chemical shift values observed in the 1H spectrum.  Two artificial neural networks have been trained and extensively tested against a non-redundant subset of the BMRB chemical shift databank [Seavey, B.R. et al. (1991) J. Biolmol. NMR, 1, 217-236 PubMed PMID: 1841696].   The most promising of the two accomplishes the analysis in two steps, grouping related amino acids together.  It presents a mean rate of success above 80% on the the test set.  The second network tested separates down to the single amino acid; it presents a mean success rate of 63%.  This tool has been used to assist in the manual assignment of peptides and proteins and can also be used tas a block in an automated approach to assignment.  The program has been called RESCUE and is made publicly available at the following URL: ftp://www.cbs.univ-montp1.fr/pub/RESCUE/

J Biomol NMR 2000 Sep;15(1):15-26.
[PubMed PMID: 10549132]

The following table lists the proteins and polypeptides along with their BMRB accession codes,  that were used to develop and test RESCUE.
 

Protein or Polypeptide BMRB Accession Code
acid phosphatase 2327
actin 3036
adenylate cyclase 1515
adrenocorticotropin 356
alamethicin 2545
alcohol dehydrogenase 1343
alpha-lytic proteinase 2619
alpha 1-purothionin 55
alpha-amylase inhibitor 1198
alpha-bungarotoxin 8
alpha-conotoxin G1 250
alpha-mating factor 1727
amphipathic alpha helix peptide 3404
anantin-A peptide 1825
annexin I 3435
antimicrobial peptide 1710
ascaris trypsin inhibitor 1 358
bacteriorhodopsin 2282
beta-endorphin 1562
bovine seminal fluid protein 1474
BSPI-2 1869
bull seminal inhibitor IIA 146
cGMP-dependant protein kinase 1757
calcitonin C 1403
carboxypeptidase B 979
caboxypeptidase inhibitor 1917
cardiotoxin VII2 2787
cecropin A 141
cell adhesion promoting peptide 1997
cellobiohydrolase 192
charybdatoxin 114
chemotactic protein P7K 779
coagulation factor X 1071
cobratoxin 1381
collagen 1709
complement protein C3a 440
complement protein C5a 2196
conotoxin GIIIA 1664
cro repressor 1743
cyclophilin 1475
defensin A 3456
designed helical protein 1445
dihydrolipoamide succinyltransferase 2546
dynorphin A 1676
aynorphin analogue 200
echistatin 2061
endothelin 1503
endothelin-3 1046
anhancer-binding protein 1336
enterotoxin 139
EGF 1337
fibronectin 2281
flavodoxin 1379
galanin 372
glucagon 140
glutaredoxin 2151
glycoprotein D-1 26
gp120 1885
growth factor 246
growth hormone releasing factor 24
hirudin 27
histone H5 30
IgG Fc region-binding protein 1120
immunogenic protein A12-9 2272
insulin B chain 1001
insulin-like growth factor-I 2498
interleukin 1-beta 1061
Jun leucine zipper domain 3394
kappa-bungarotoxin 1675
kininogen 1588
kistrin 2856
leiurotoxin I 408
lipoate acetyltransferase 1756
lysozyme 1093
male-associated protein 1500
melanin concentrating hormone 1677
metallothionein 248
microglobulin 3078
motilin 754
natriuretic peptide 1201
neocarzinostatin 1766
neuropeptide Y 548
neurotensin 1697
neurotoxin I 275
neutrophil NP-5 41
nisin 2279
nucleic-acid-binding protein 1640
nucleocapsin protein 1656
ocytocin 2948
ovomucoid third domain 1374
P22 arc repressor 395
p55F1 zinc fingerlike domain 252
pancreatic polypeptide 2223
vpq polypeptide 810
Xfin-31B 2328
prothrombin 2013
parvalbumin 144
parathyroid-hormone-related protein 1666
phosphocarrier protein HPr 2030
phospholipid transfer protein 2065
pituitary growth factor 2197
protein L 3466
proteinase inhibitor IIA 53
putidaredoxin 2278
rubredoxin 1991
sapecin 1209
sarafotoxin-S6b 1700
serum albumin 1616
seven-iron ferredoxin 1133
soybean proteinase inhibitor 1495
SW15 zinc finger 780
synthesized signal peptide 1137
tachyplesin I 1135
tendamistat 1642
thymosin beta-4 1065
toxin ATX III 3485
toxin AaH III 2283
toxin AaH IT 1478
toxin BDS-I 480
toxin RP III 300
transcription factor IIIA 420
transcription factor LFB1 1414
transcriptional activator ADR1 1496
transcriptional activator GAL4 1517
transcriptional regulator GCN4 1447
transforming growth factor 162
transforming growth factor alpha a 517
troponin I 2116
trypsin inhibitor CMTI-I 199
trypsin inhibitor II  397
tubulin binding peptide 1338
tubulin-beta 1817
ubiquitin 2573
vasoactive intestinal peptide 1652
viral coat protein 1635
Xfin-31C 2329
ZFY switch 1911