ライフサイエンスコーパス: protein database

1 m other species in the GenBank NR nucleotide/protein database.

2 18 chitinase-like proteins in the Drosophila protein database.

3 sts of true positives from the non-redundant protein database.

4 lyzed, 46 were identified by matching to the protein database.

5 when run against the complete non-redundant protein database.

6 A with motif databases and the non-redundant protein database.

7 erformed by searching an Internet-accessible protein database.

8 pha-actinin sequences deposited in the Swiss Protein Database.

9 for unique retrieval of this enzyme from the protein database.

10 oil based on the phi, psi distributions in a protein database.

11 d by searches of the data against an E. coli protein database.

12 y digested peptides derived from a reference protein database.

13 on-isobaric mutations for every residue in a protein database.

14 ching top-down tandem mass spectra against a protein database.

15 ct from the members available in the current protein database.

16 st in silico produced spectra derived from a protein database.

17 11% of BESs have homology to the Arabidopsis protein database.

18 notated and classified functionally based on protein databases.

19 compared with conventional searches against protein databases.

20 xample, annotation of microarray data and of protein databases.

21 provide links to PubMed abstracts and major protein databases.

22 build motifs that could be searched against protein databases.

23 on the basis of blastX searches against all protein databases.

24 identification using tandem mass spectra and protein databases.

25 ction of CIN85 novel-interacting partners in protein databases.

26 ence of p300 have been identified in current protein databases.

27 and searched against on-line nucleotide and protein databases.

28 ags that do not match entries in the DNA and protein databases.

29 and ORF3 were found in the nucleic acid and protein databases.

30 significant similarity to members of DNA or protein databases.

31 s of similarity searches with nucleotide and protein databases.

32 ching of the spectral data against bacterial protein databases.

33 s relies heavily on the presence of complete protein databases.

34 ), PO4(3-)) that are most frequently seen in protein databases.

35 o acid sequences are unlike any published in protein databases.

36 r and compilation of information from online protein databases.

37 s, as well as external links to sequence and protein databases.

38 cted by covariance analyses of two-component protein databases.

39 s with different levels of representation in protein databases.

40 at incorporates structural bias derived from protein databases.

41 similarity to any other sequences present in protein databases.

42 on through homology searches at nonredundant protein databases.

43 erived from the structural classification of proteins database.

44 uccessor to the Structural Classification of Proteins database.

45 We analyzed structural data of a membrane proteins database.

46 Republished from Current BioData's Targeted Proteins database.

47 oto Encyclopedia of Genes and Genomes (KEGG) protein database; 2) a web viewing application that disp

48 Based on an annotated human cardiac protein database, 62% have at least one PTM (phosphoryla

49 abase retrieval algorithm (Retriever), MySQL protein databases, a file/data manager, and a project tr

50 tricted coding sequences not found in public protein databases, a web-based WU-BLAST search tool that

51 ts of the SCOP (Structural Classification of Proteins) database, a gold standard for protein structur

52 information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Univ

53 nslated DNA sequence to each sequence in the protein database, allowing gaps and frameshifts.

54 Protein database analyses of the peptides, CVSNPRWKC and

55 as identified by peptide microsequencing and protein database analysis as troponin I (TnI).

56 ionization mass spectrometry (MALDI-MS) and protein database analysis.

57 With a newly designed index structure for protein database and associated optimizations in BLASTP

58 In parallel to milk protein database and de novo searches, the retention tim

59 y maintaining a comprehensive, non-redundant protein database and for creating a quarterly release of

60 against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica

61 iver biopsy protein digest using the Huh-7.5 protein database and the accurate mass and time tag stra

62 one for comparing the query sequence with a protein database and the other for comparing the query w

63 sequence-structure motifs as observed in the protein database and, by representing overlapping motifs

64 , 78% had similarity matches to sequences in protein databases and 83% had exact expressed sequence t

65 Bank nucleotides patent class and the patent protein databases and contain value-added annotations fr

66 k all peptides in public viral and bacterial protein databases and identify potential molecular mimic

67 We describe how to use public protein databases and molecular modeling programs to sel

68 The widening function annotation gap in protein databases and the increasing number and diversit

69 ndem mass spectra to peptides derived from a protein database, and (2) mapping assigned peptides to p

70 A queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic

71 ected from the same protein mixture, a FASTA protein database, and a selection of possible PTMs, the

72 m all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classif

73 ed to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMe

74 75 are tentatively assigned to proteins in a protein database, and these proteins are characterized b

75 d methods for data mining of the literature, protein databases, and knowledge bases (IT.Omics LSGraph

76 were obtained through SEQUEST searches of a protein database appended with its decoy (reversed seque

77 otechnology Information (NCBI) non-redundant protein database approaches 90%.

78 A searchable protein database, ARABI-COIL, was established that integ

79 l packings and topologies with no analogs in protein database are identified.

80 However, because the EST and protein databases are constantly growing, in many cases

81 roteomic analyses of higher eukaryotes where protein databases are large.

82 ustering speed is needed because the size of protein databases are rapidly growing and many applicati

83 initions in the Structural Classification of Proteins Database are used, so that we can view all pair

84 esults, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST alg

85 r for Biotechnology Information nonredundant protein database as likely parallel beta-helices.

86 integrates and links the main nucleotide and protein databases as well as many other specialist molec

87 we have constructed an Alternatively Spliced Proteins database (ASP) from analysis of human expressed

88 Protein entries in databases such as Entrez Protein database at NCBI contain information about publi

89 P5 was not homologous to any sequence in the protein database at the National Center for Biotechnolog

90 st and flexible program for clustering large protein databases at different sequence identity levels.

91 forms similarity searches of the NCBI Entrez Protein Database based on domain architecture, defined a

92 MS platforms and construction of customized protein databases based on RNA-Seq data with or without

93 y when searching MS/MS spectra against large protein databases because of their atypical lengths (e.g

94 which scale linearly in the size of the full protein database being searched.

95 Binary subcomplexes in proteins database (BISC) is a new protein-protein intera

96 andem mass spectrometry requires a reference protein database, but these are only available for model

97 h those derived theoretically from the Swiss Protein Database by computer-based comparisons.

98 The Yeast Protein Database can be found on the Web at http://www.p

99 hich does not have any known homologs in the protein databases, causes cells to form biofilms that ar

100 A high-quality liver protein database containing 5,920 unique protein identif

101 rotein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences cover

102 e brain vasculome with representative plasma protein databases demonstrated significant overlap, sugg

103 g novel peptides by searching the customized protein database derived from RNA-Seq data.

104 r previous study showed that sample-specific protein databases derived from RNA-Seq data can better a

105 Optimization of sample preparations and protein database developments are enhancing the quantity

106 A search of protein databases disclosed that the P47 peptide mass pr

107 cient for matching nanospectra against small protein databases, e.g., protein identification in bacte

108 ein count is not inflated by variants in the protein database, eliminating approximately 25% of redun

109 all SWISS-PROT, TrEMBL, Genpept and Ensembl protein database entries are now possible with run times

110 juvenile Fugu tissues, 74% of which matched protein database entries.

111 By screening the public protein database for Atg32 homologues, we identify Bcl2-

112 spectrometry are searched directly against a protein database for identification of the protein from

113 sequencing of expressed mRNA can generate a protein database for mass spectrometry-based identificat

114 PHI-BLAST searches a protein database for other instances of the input patter

115 sequence information can be used to search a protein database for protein identification.

116 d its analogues to define motifs to search a protein database for structural homologues of PLP139-151

117 ng an automatic SEQUEST search of the single protein database for this antibody and extensive manual

118 We established criteria for searching protein databases for prion candidates and found several

119 Man (OMIM) human genetics database and other protein databases for the selection of attractive target

120 a from NCBI's SNP database (dbSNP), gene and protein databases from Entrez, protein structures from t

121 STX search with all tags of the nonredundant protein database gave only 161 unique significant matche

122 mass spectra are often searched against huge protein databases generated from genomes or RNA-Seq data

123 The availability of large protein databases generated from sequences of hundreds o

124 The recent growth in protein databases has revealed the functional diversity

125 illion protein sequences in the nonredundant protein database have no structural information, it is d

126 ently in use for querying MS/MS data against protein databases have been optimized on the basis of ma

127 unction relationships is presented: the Heme Protein Database (HPD).

128 quence similarity searches of nucleotide and protein databases identified the first homologs of MAGP1

129 and other known invasion genes when DNA and protein databases in GenBank were searched.

130 ries increases linearly as the volume of the protein databases increase.

131 The UniProt Reference Clusters (UniRef100) protein database is used as the reference database for t

132 Comparing two protein databases is a fundamental task in biosequence a

133 matching tandem mass spectra (MS/MS) against protein databases is a widespread tool in mass spectrome

134 dress this deficit, functional annotation in protein databases is often inferred by sequence similari

135 The SCOP (Structural Classification of Proteins) database is a comprehensive ordering of all pr

136 novel peptide detection with the customized protein database, is necessary.

137 Because AidA has no homologs in the protein databases, its discovery provided no clues as to

138 Clustering large protein databases like the NCBI Non-Redundant database (

139 This database, the Ligand-Protein DataBase (LPDB), is designed to allow the select

140 junctions identified from RNA-Seq data make protein database more complete and sample-specific.

141 equences of these unigenes against different protein databases, nearly 60% of them were annotated and

142 In contrast, RNA expression and protein databases need to be able to handle very high di

143 The Nuclear Protein Database (NPD) is a curated database that contai

144 ecific databases, the beta-lactam-resistance protein database of A. baumannii (BRPDAB).

145 mparison and clustering of the non-redundant protein database of over 560,000 sequences on a high-end

146 he CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of

147 A customized protein database on the basis of RNA-Seq data is thus pr

148 we have introduced a non-redundant reference protein database, PIR-NREF.

149 integrates and links the main nucleotide and protein databases plus many other specialized databases.

150 integrates and links the main nucleotide and protein databases plus many other specialized molecular

151 egrating and linking the main nucleotide and protein databases plus many specialised databases.

152 integrates and links the main nucleotide and protein databases plus many specialized databases.

153 egrating and linking the main nucleotide and protein databases, plus many specialised databases.

154 ein products of which have clear homologs in protein databases, predictions were recomputed by Fgenes

155 The Arabidopsis Nucleolar Protein Database provides information on 217 proteins id

156 teins (which make up >65% of the large-scale protein databases) provides a valuable tool for function

157 miRNAs were also elucidated from the EST and protein databases, providing additional evidence for the

158 Therefore, the protein database required for the interpretation of spec

159 of DNA reads from such samples to reference protein databases requires long run-times, and short rea

160 BLASTP searches of the NCBI protein database revealed clear homologies in three pept

161 first 20 amino acid residues of Tpn with the protein databases revealed a high degree of homology to

162 Comparisons with protein databases revealed homologies to (a) ubiquitin,

163 A search of the protein databases revealed sequence similarities to O-me

164 he GSSs with sequences in the public DNA and protein databases revealed that 107 contigs (26%) displa

165 Comparison of Tnk1 to available sequences in protein databases reveals that it is most homologous to

166 definitions in Structural Classification of Proteins Database (SCOP) in order to map pairs of adjace

167 rmat or enter a Structural Classification of Proteins database (SCOP)/PDB identifier for which NCI id

168 tes the need for specific parametrization of protein database search algorithms.

169 To test this idea, a protein database search for potential MART-1 epitope mim

170 The PSI-BLAST protein database search program derives the column score

171 A version of the BLAST protein database search program, modified to employ this

172 ggest possible improvements to the PSI-BLAST protein database search program.

173 A protein database search revealed that AlgZ is homologous

174 m for restriction to certain autoantigens, a protein database search was done for homologies with seq

175 ypeptides from C. elegans and S. pombe, in a protein database search.

176 Protein database searches demonstrate Tdd-4 encoded prot

177 been designed and implemented such that most protein database searches return within a few seconds.

178 man, mouse, rat and Drosophila muskelins and protein database searches revealed a novel highly conser

179 DNA and protein database searches revealed that SEND32, SEND35,

180 Protein database searches revealed that SusE had limited

181 web-based email alert system for monitoring protein database searches using HMMER and Blast-P, nucle

182 Protein database searches using the consensus PDZ-bindin

183 Protein database searches were performed using the masse

184 Protein identification is carried out using protein database searches with search scoring systems, w

185 loss of information compared to conventional protein database searches.

186 ion of domain and functional predictions for protein database searches.

187 ope sequence data so as to enable successful protein database searches.

188 Protein database searching and molecular modeling reveal

189 An example of the use of protein database searching of a partial peptide sequence

190 -generated partial sequence information with protein database searching techniques are presented.

191 Using this motif as a protein database searching tool, we find that it is pres

192 -desorption ionization mass spectrometry and protein database searching, the 40-kilodalton ligand was

193 ied by mass spectrometry in combination with protein database searching.

194 The sequences obtained are used for protein database searching.

195 ected tandem mass spectrometry combined with protein database searching.

196 ntial residues for channel functions in Orai proteins, database searching also identifies a putative

197 le the data and interrogate the nonredundant protein database, searching for a close match.

198 The protein database section features important updates on t

199 An alignment of 67 SLN sequences from the protein databases shows that 19 of them contain a cystei

200 acid databases and in all six frames to the protein databases: Sixeen clones could be assigned to kn

201 th the following novel features: (1) a novel protein database structure containing extensive preindex

202 Analysis of protein databases suggests most eukaryotic genomes encod

203 technology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Labora

204 the residue probability distributions in the protein database; the decoupling of the distance and env

205 and hood have no structural precedent in the protein database, therefore representing new folds.

206 r for Biotechnology Information nonredundant protein database to determine the phylogenetic relatedne

207 Most of these computer programs use a protein database to match peptide sequences to the obser

208 the millions of decapeptides contained in a protein database to rank and predict the most stimulator

209 es sequence similarity search against custom protein databases to identify protein coding regions, st

210 g BLAST similarity comparisons to the public protein databases to identify putative genes.

211 ch, was applied to >13,000 such domains from protein databases to identify residue contacts between t

212 ent mass spectrometry (MS/MS), and searching protein databases to identify the proteins from which th

213 r proteins, using predictive analysis from a protein database, to see whether this may be related to

214 A search of the protein databases uncovered many additional putative pho

215 protein that is not present in an annotated protein database using a "top-down" approach with a quad

216 ived from the MS/MS data was compared with a protein database using BLAST software, revealing homolog

217 proximately 280000 entries in a nonredundant protein database using SEQUEST.

218 BLAST searches of the NCBInr protein database using the amino acid sequence of MiSp1-

219 Markov model profile-to-profile searches in protein databases using endoplasmic reticulum lumen prot

220 Bayesian algorithm to identify proteins from protein databases using mass spectrometric peptide mappi

221 important for those applications that search protein databases using the de novo sequencing results.

222 programs that primarily interact with large protein databases via precisely these tools.

223 A macaque protein database was assembled and used in the identific

224 ss to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found i

225 imilar amino acid sequences retrievable from protein databases, we have identified the following moti

226 similarities to viruses in the nonredundant protein database were selected.

227 rimental data can be used interactively with protein databases when the modified protein of interest

228 ication programs are restricted to searching protein databases where data are often lagging behind th

229 ation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequ

230 a are not present in most publicly available protein databases, which only include sequences in Swiss

231 zinc metalloproteases can be founded in the protein database with a cysteine at a similar location,

232 This program can efficiently cluster a huge protein database with millions of sequences.

233 t as advances in sequencing technology flood protein databases with an exponentially growing number o

234 Searches of the major public protein databases with core and linker chicken and human

235 tigen can be rapidly identified by searching protein databases with the mass spectral data in conjunc

236 The Yeast Protein Database (YPD) is a curated database for the pro

237 The Yeast Protein Database (YPD) is a database for the proteins of