ライフサイエンスコーパス: data bank

1 sion), and structural data from PDB (Protein Data Bank).

2 n from F1 structures 2HLD1 and 1H8E (Protein Data Bank).

3 in unique antibody structures in the Protein Data Bank.

4 ds from similar binding sites in the Protein Data Bank.

5 tructural patterns within the entire Protein Data Bank.

6 a Bank and map-derived models in the Protein Data Bank.

7 aptured by hundreds of structures in Protein Data Bank.

8 ures determined and deposited to the Protein Data Bank.

9 ycine amino acids in proteins in the protein data bank.

10 eir sources: DrugBank, BindingDB and Protein Data Bank.

11 the prospectively maintained National Trauma Data Bank.

12 ndly and is integrated into the RCSB Protein Data Bank.

13 ay structures of DNA duplexes in the Protein Data Bank.

14 e Control and Prevention and National Trauma Data Bank.

15 itor, acetazolamide, is available in Protein Data Bank.

16 Informatisees et Validees en Transplantation data bank.

17 structures of human proteins in the Protein Data Bank.

18 ctures of epigenome readers from the Protein Data Bank.

19 ty rates using data from the National Trauma Data Bank.

20 resolution ribozyme structure in the Protein Data Bank.

21 homologous structure families in the Protein Data Bank.

22 centers participating in the National Trauma Data Bank.

23 mistic thin filament models from the Protein Data Bank.

24 ives provided by the National Practitioner's Data Bank.

25 1 structure has no equivalent in the Protein Data Bank.

26 American College of Surgeons National Trauma Data Bank.

27 in-RNA structures retrieved from the Protein Data Bank.

28 2707 different ligand types from the Protein Data Bank.

29 lergens and proteins reported in the Protein Data Bank.

30 tem, and mirrors the contents of the Protein Data Bank.

31 -antigen cocrystal structures in the Protein Data Bank.

32 , and a bioinformatics screen of the Protein Data Bank.

33 s (ligand fragments) observed in the Protein Data Bank.

34 ed in the structural database of the Protein Data Bank.

35 in spectra in the Protein Circular Dichroism Data Bank.

36 th macromolecular structures and the Protein Data Bank.

37 res, designated 2JMH and 2JRK in the Protein Data Bank.

38 taining molecules deposited into the Protein Data Bank.

39 ue structures are represented in the Protein Data Bank.

40 tribute complications to the National Trauma Data Bank.

41 t study of patients from the National Trauma Data Bank.

42 have close homology templates in the Protein Data Bank.

43 ng data contained within the National Trauma Data Bank.

44 ligand atom pairs from mining of the Protein Data Bank.

45 500 protein kinase structures in the Protein Data Bank.

46 nt JSON representation to the entire Protein Data Bank.

47 76 distinct kinases available in the Protein Data Bank.

48 extracted from the 2007-2012 National Trauma Data Bank.

49 t as well as structure data from the Protein Data Bank.

50 >97% of the KDO/KO structures in the Protein Data Bank.

51 that are made available through the Protein Data Bank.

52 tinct GroEL crystal structure in the Protein Data Bank.

53 37 have folds not represented in the Protein Data Bank.

54 ther proteins and mRNAs are described in the data banks.

55 ESV proteins found no matches in the protein data banks.

56 When applied to the entire Protein Data Bank, 164 514 druggable cavities were identified an

57 vel I/II TCs included in the National Trauma Data Bank 2007-2010.

58 retrospective review of the National Trauma Data Bank (2008-2014) was performed and patients < 21 ye

59 matching substructures in the entire Protein Data Bank, along with a statistical significance estimat

60 tructures, and databases such as the Protein Data Bank, also implies large scale structural similarit

61 most frequently observed PTMs in the Protein Data Bank and all types of phosphorylation.

62 able PPI structures deposited in the Protein Data Bank and allows users to upload their own custom st

63 protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store thi

64 EGFR and mTOR were obtained from the protein data bank and docked with 23 3D PubChem structures of fu

65 We search through the entire Protein Data Bank and identify several sequentially nonhomologou

66 ural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Ban

67 s who were registered in the National Trauma Data Bank and met inclusion criteria.

68 I who were registered in the National Trauma Data Bank and met the inclusion criteria.

69 0 crystal data sets deposited in the Protein Data Bank and show that sharpening improves the electron

70 nst the RNA structures in the entire Protein Data Bank and the abundances of them are estimated.

71 lly from the current releases of the Protein Data Bank and the Uniprot Knowledgebase; this core is co

72 whose structure is available in the Protein Data Bank and which exhibits one or more helices at the

73 ures in test sets extracted from the Protein Data Bank and would be useful starting points in modelin

74 main protein structures found in the Protein Data Bank) and ART structures and pockets, the widesprea

75 olecular structures available in the Protein Data Bank archive and the tools that are available at th

76 ximately 2% of the structures in the Protein Data Bank are from eukaryotic parasites and less than 0.

77 protein structures deposited in the Protein Data Bank are of membrane proteins.

78 structures have been archived in the Protein Data Bank as compared to the more than 100 000 structure

79 uncertainty for both SN within the Emissions Data Bank as well as nvPM mass within the new regulatory

80 me, GTK/KAT I, is listed in mammalian genome data banks as CCBL1 (cysteine conjugate beta-lyase 1).

81 ved from structures deposited in the Protein Data Bank, based on sequence similarly, fit of stem atom

82 nificant result that agrees with our Protein Data Bank-based backbone sampling and all-atom simulatio

83 to many such situations and combines Protein Data Bank-based torsional optimization with real-space r

84 I who were registered in the National Trauma Data Bank between 2009 and 2011.

85 s who were registered in the National Trauma Data Bank between 2009 and 2011.

86 The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magne

87 results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending p

88 Here using a large whole-genome sequencing data bank, cancer registry and colorectal tumour bank we

89 The conformational dynamics data bank (CDDB) is a database that aims to provide comp

90 00 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing

91 ydroxy-3,5-dimethylphenyl)methanone (Protein Data Bank chemical component 0XV) was determined to 2.87

92 he peptide contained residues 20-45 (Protein Data Bank code 1BEA), and a C29D substitution was includ

93 ed for the P450 2D6 Met-374 variant (Protein Data Bank code 2F9Q).

94 small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other Mar

95 toms in the initial vSGLT structure (Protein Data Bank code 3DH4).

96 erichia coli isoprenoid synthesis H (Protein Data Bank code 3F7T) as a template for homology modeling

97 -yl)-2-(pyridin- 3-yl)ethanone (UDO; Protein Data Bank code 3ZG2) and N-[4-(trifluoromethyl)phenyl]-N

98 -4-piperi-dyl]p yridin-3-amine (UDD; Protein Data Bank code 3ZG3).

99 s 2C8 and 2C9, the atomic structure (Protein Data Bank code 4GQS) of cytochrome P450 2C19 complexed w

100 on representative proteins from the Protein Data Bank, comparing secondary structure and disorder pr

101 n all nucleic acid structures in the Protein Data Bank confirm the efficiency and robustness of the s

102 rvey of two-way RNA junctions in the protein data bank confirms that junction residues have a strong

103 Whereas the Protein Data Bank contains some 100,000 globular protein and 3,0

104 DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water

105 Protein Data Bank data mining using the HippDB database indicate

106 onding drug-target structures in the Protein Data Bank database, and 15 out of the 18 had been proved

107 ble in the Nucleic Acid Database and Protein Data Bank databases.

108 s are related to ones already in the Protein Data Bank.) DeepMind's success generated significant pub

109 of protein-protein complexes in the Protein Data Bank, docking templates can be found for complexes

110 essors either as single files or as complete data bank downloads.

111 ives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facili

112 uctures deposited in the Electron Microscopy Data Bank (EMDB) at higher than 4- angstrom resolution w

113 of D12A BsPFK have been determined (Protein Data Bank entries 4I36 and 4I7E , respectively), and bot

114 Dab to update weekly, reflecting new Protein Data Bank entries and the availability of new sequence d

115 SCOPe 2.06 contains 77,439 Protein Data Bank entries, double the 38,221 structures classifi

116 increased our coverage of available Protein Data Bank entries.

117 ms that represent approximately 3800 Protein Data Bank entries.

118 sis of a set of protein spectra with Protein Data Bank entries.

119 rotein structure (residues 15 to 41; Protein Data Bank entry 1CWX) indicated that the residues G33 an

120 solved structure of MMP-3cd.TIMP-1 (Protein Data Bank entry 1UEA), we see substantial differences at

121 P450 3A4 (CYP3A4) crystal structure (Protein Data Bank entry 1W0E) to predict the sites of metabolism

122 was determined at 2.7 A resolution (Protein Data Bank entry 2PAJ ).

123 ive site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9 ).

124 cl-XL protein and a Bax BH3 peptide (Protein Data Bank entry 3PL7).

125 cture of the archaeal NCX homologue (Protein Data Bank entry 3V5U ), we introduced cysteine residues

126 structure bound to PEP is reported (Protein Data Bank entry 4I4I ), and it exhibits a shifted struct

127 ucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text minin

128 ns lack of similar structures in the Protein Data Bank even on a personal computer.

129 Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of t

130 e in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER.

131 s are annotated and transformed into protein data bank files, which are downloadable by researchers w

132 web server that searches the entire Protein Data Bank for a given substructure defined by a set of a

133 claims reported to the National Practitioner Data Bank for events in the outpatient setting was simil

134 gands for hundreds of targets in the Protein Data Bank for which similar experimental information is

135 ta, provided as a set of models in a Protein Data Bank format.

136 rotein, DNA or RNA structure in PDB (Protein Data Bank) format.

137 ns and show that no structure in the Protein Data Bank forms a link of this type.

138 on-capsid protein complexes from the Protein Data Bank found 418 generic protein-protein interfaces t

139 0 to 17 years old using the National Trauma Data Bank from January 1, 2007, to December 31, 2012.

140 e carried out a broad search of RIP sequence data banks from angiosperms in order to study their main

141 (varphi,psi) distributions from the Protein Data Bank further justifies the inclusion of many-body e

142 t, gene number proposition, genetic mapping, data banks, gene-disease maps, catalogs of human genes a

143 e of the valuable information in the Protein Data Bank generated by structural genomics projects but

144 non-redundant OMBB structures in the Protein Data Bank, half have been solved during the past 5 years

145 te of novel pockets deposited in the Protein Data Bank has been decreasing steadily over the recent y

146 t a quarter of all structures in the Protein Data Bank; however, available protein complexes cover le

147 he published IpaD crystal structure (Protein Data Bank ID 2j0o) how a multimer of IpaD would be incor

148 channel in the open state is known (Protein Data Bank ID code 2R9R).

149 reviously determined NTR1 structure (Protein Data Bank ID code 4GRV) in the ligand-binding pocket and

150 ryo-EM structure of amphibian TRPV4 (Protein Data Bank ID code 6BBJ), which appears to be in a differ

151 m formin binding protein 28 (FBP28) (Protein Data Bank ID: 1E0L) and its full-size, and singly- and d

152 yielded two different crystal forms (Protein Data Bank identifiers [PDB ID], 3LQ6 and 3LQE).

153 is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt.

154 The Protein Data Bank in Europe (PDBe), a founding member of the Wor

155 MDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory f

156 The Protein Data Bank in Europe (pdbe.org) is a founding member of t

157 The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a p

158 The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the

159 The Protein Data Bank in Europe accepts and annotates depositions of

160 tatic structures of a protein in the Protein Data Bank in order to extract the progression of structu

161 The National Trauma Data Bank is a voluntary data repository managed by the

162 f membrane protein structures in the Protein Data Bank is becoming significant and growing.

163 Each year, a data bank is developed by fermenting authentic apples ju

164 Our results strongly argue that the Protein Data Bank is now sufficiently large to enable proteins t

165 ssigned to the encoded protein in the genome data bank, is a CCBL2 (synonym KAT III).

166 rs participating in the 2010 National Trauma Data Bank (January 1 to December 31, 2010) were used to

167 tures are currently available in the Protein Data Bank, largely owing to inefficiencies in protein pr

168 Screening of the Protein Data Bank led to identification of a recurring structura

169 r one other protein structure in the Protein Data Bank, namely, YokD from Bacillus subtilis.

170 ents from 2003 to 2015), the National Trauma Data Bank (NTDB) (5755095 patients from 2003 to 2014), a

171 e from Lyon, France, and the National Trauma Data Bank (NTDB) of the United States.

172 ent years (2007-2009) in the National Trauma Data Bank (NTDB).

173 crystal structures deposited in the Protein Data Bank of 32 different receptors from families scatte

174 uropean Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage.

175 n Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ).

176 the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage.

177 And thanks in part to the large Protein Data Bank of known structures, predicting protein struct

178 An in vivo human tissue compliance data bank of the gastrointestinal tract was produced.

179 he entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the

180 The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5

181 obtained from the Protein Circular Dichroism Data Bank (PCDDB).

182 on simulated data of GroEL from the Protein Data Bank (PDB ID:1KP8) showed that our parallel SAG-bas

183 ere are few pMHC-I structures in the Protein Data Bank (PDB) (especially considering the total number

184 n, corrections have been made to the Protein Data Bank (PDB) accessions in the 'Data availability' se

185 spatial information available in the Protein Data Bank (PDB) along with the mutational data in the Ca

186 However, with the steady growth of Protein Data Bank (PDB) and available PTM sites, it is now possi

187 yloid fibril structures found in the Protein Data Bank (PDB) and numerous clinical trials, therapeuti

188 and binding sites extracted from the Protein Data Bank (PDB) and small organic molecules from the Cam

189 xample, by combining the data in the Protein Data Bank (PDB) and the Catalogue of Somatic Mutations i

190 ating the spatial information in the Protein Data Bank (PDB) and the mutational data in the Catalogue

191 g problem because of the size of the Protein Data Bank (PDB) archive.

192 Published integrin structures in the Protein Data Bank (PDB) are examined to gain insights into integ

193 use the protein structures from the Protein Data Bank (PDB) as templates.

194 d structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user

195 The Protein Data Bank (PDB) contains >67 000 entries containing enzy

196 The Protein Data Bank (PDB) contains a wealth of data on nonbonded b

197 The Protein Data Bank (PDB) currently holds over 140 000 biomolecula

198 complexes currently available in the Protein Data Bank (PDB) database, revealing a great diversity of

199 ease of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of struct

200 d small molecule components found in Protein Data Bank (PDB) entries.

201 g loop (LL conformation), similar to Protein Data Bank (PDB) entry 1CMK , and a helix-turn-helix stru

202 developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the aut

203 reate the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge

204 t, and oligomeric states to mine the Protein Data Bank (PDB) for potentially similar protein structur

205 orresponding coordinate files in the Protein Data Bank (PDB) format.

206 sic use, requiring only two files in Protein Data Bank (PDB) format.

207 spatial structures maintained by the Protein Data Bank (PDB) into evolutionary groups of protein doma

208 Benchmark tests against the Protein Data Bank (PDB) N-linked glycan library and PDB homologo

209 The Protein Data Bank (PDB) now contains more than 120,000 three-dim

210 easy downloads of IBIS data for all Protein Data Bank (PDB) protein chains and the results for each

211 n of membrane protein entries in the Protein Data Bank (PDB) remains <4%.

212 available Apo EPK structures in the protein data bank (PDB) revealed four unique structural conforma

213 sis of structural information in the Protein Data Bank (PDB) shows how 5-methylcytosine (5mC) can be

214 et al., using the limited number of protein data bank (PDB) structures available at that time, repor

215 can be used for databases other than Protein Data Bank (PDB) such as Protein families database or Clu

216 rization of 10,245 beta-turns in the protein data bank (PDB) suggested that trans-pyrrolidine-3,4-dic

217 n programming interface for the RCSB Protein Data Bank (PDB) that allows search and data retrieval fo

218 trieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide's f

219 ANCHOR includes a Protein Data Bank (PDB) wide database of pre-computed anchor res

220 in crystal structures present in the Protein Data Bank (PDB) with a focus on PDE-ligand interactions.

221 ctural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural da

222 crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB a

223 re generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has rev

224 tabase, ProCarbDB, which, unlike the Protein Data Bank (PDB), clearly distinguishes between the compl

225 owth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to ol

226 Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource

227 Ms that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy.

228 tabase (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-dat

229 100 000 structures available in the Protein Data Bank (PDB), of which approximately 30% are protein-

230 twork has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative confo

231 ) and the spatial information in the Protein Data Bank (PDB), SpacePAC is able to identify novel muta

232 f to identify all RLM domains in the Protein Data Bank (PDB), thus finding they constitute about 20%

233 ctural knowledge, extracted from the Protein Data Bank (PDB), underlies numerous potential functions

234 of a coronavirus-related resource at Protein Data Bank (PDB)-101, the education portal of the RCSB PD

235 have been resolved and deposited in Protein Data Bank (PDB).

236 reely distributed by the open-access Protein Data Bank (PDB).

237 f congeneric ligand complexes in the Protein Data Bank (PDB).

238 e of RNA crystal structures from the Protein Data Bank (PDB).

239 ptimally modeled are abundant in the Protein Data Bank (PDB).

240 and RNA structures deposited in the Protein Data Bank (PDB).

241 cocrystal structures present in the Protein Data Bank (PDB).

242 no structural analogues found in the Protein Data Bank (PDB).

243 re within structured proteins in the Protein Data Bank (PDB).

244 and protein-protein complexes in the Protein Data Bank (PDB).

245 s to sequences and structures in the Protein Data Bank (PDB).

246 stal structures are available in the protein data bank (PDB).

247 aces extracted from complexes in the Protein Data Bank (PDB).

248 with 3D structures deposited in the Protein Data Bank (PDB).

249 rotein structures, released from the Protein Data Bank (PDB).

250 s based on proteins deposited in the Protein Data Bank (PDB).

251 g(II) binding sites available in the protein data bank (PDB).

252 ding "hot" and "warm" spots from the Protein Data Bank (PDB).

253 ved in 3D structures archived in the Protein Data Bank (PDB).

254 H-bonds than regular proteins in the Protein Data Bank (PDB).

255 s (ECOD) database] or 20,398 chains [Protein Data Bank (PDB)].

256 sting data based on crystallography (Protein Data Bank, PDB) can be used to discriminate between inte

257 med a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cas

258 f pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites.

259 r-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute).

260 Mining of the Protein Data Bank provides an abundance of structures in which G

261 Extensive analysis of the Protein Data Bank provides strong support for a catalytic role o

262 of domain-domain interactions in the Protein Data Bank, providing molecular details for such interact

263 NMR) techniques and deposited in the Protein Data Bank, rather than on ensembles specifically generat

264 ratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that p

265 The RCSB Protein Data Bank (RCSB PDB) provides access to 3D structures of

266 ratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to th

267 ratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query,

268 ratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique user

269 ratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for t

270 protein structures deposited in the Protein Data Bank resulted in 874 entries, consisting of 194 uni

271 he Cambridge Structural Database and Protein Data Bank reveal geometric preferences of some oxygen an

272 luding unpublished structures in the Protein Data Bank, revealed extensive variation in the relative

273 of a TEL fragment, deposited in the Protein Data Bank, revealed that the CID consists of two alpha-h

274 ehensive topological analysis of the Protein Data Bank reveals several novel structures including kno

275 her examination of structures in the Protein Data Bank reveals that there is a great disparity betwee

276 A statistical analysis of the Protein Data Bank reveals that this mode of interaction is a com

277 s protein-adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragm

278 grated computational approach of the Protein Data Bank structure analysis and atomistic molecular dyn

279 Starting from the native Protein Data Bank structure, nine (meta)stable states of the sys

280 s non-protein coding RNA, <2% of the protein data bank structures comprise RNA.

281 Analysis of the existing Protein Data Bank structures of Bcl-xL in both bound and unbound

282 UniProt identifiers and (optionally) Protein Data Bank structures.

283 alis alpha-actinin epitopes with proteins in data banks, such as Tritrichomonas suis, Candida albican

284 ments from protein structures in the Protein Data Bank that are similar to the 3D arrangements of kno

285 ogether molecular fragments from the Protein Data Bank that best fit experimental RDCs from samples w

286 ve interoperability between the RCSB Protein Data Bank, the NCBI, and the UniProtKB data resources an

287 ratory for Structural Bioinformatics Protein Data Bank, the US data center for the global PDB archive

288 f membrane protein structures in the Protein Data Bank, there are many transmembrane domains that app

289 uses similarity to sequences in the Protein Data Bank to infer annotations at the output level, and

290 of helical protein interfaces in the Protein Data Bank to obtain a snapshot of how helices that are c

291 oordinates of 22 structures from the Protein Data Bank to perform sequence and structural alignments,

292 nked an extract of the National Practitioner Data Bank to the Medicare Data on Provider Practice and

293 cluding PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase

294 umber of unique binding sites in the Protein Data Bank was much slower than the growth rate of the nu

295 The National Trauma Data Bank was queried (version 6.2, 2001-2006) for infor

296 Using data from the National Practitioner Data Bank, we analyzed 66,426 claims paid against 54,099

297 centers participating in the National Trauma Data Bank were identified using International Classifica

298 mination of protein complexes in the Protein Data Bank where alpha-helices or beta-strands form criti

299 ECTS: Trauma patients in the National Trauma Data Bank with a hospital length of stay greater than 2

300 , a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the depositi