ライフサイエンスコーパス: root mean square deviation

1 ilarity between their backbone atoms (0.96-A root mean square deviation).

2 nd recoverin in the absence of target (<1.8A root-mean-square deviation).

3 y has been reduced to less than 0.20 e rmsd (root-mean-square deviation).

4 NMR native structure to within 1A main-chain root mean square deviation.

5 nced by smaller temporal fluctuations in the root mean-square deviation.

6 -ray ligand positions within 2.0A heavy atom root-mean-square deviation.

7 8) stabilized by three structural zinc ions (root mean square deviation 0.30 +/- 0.04 A) along with a

8 imilar to that of the E. coli apical domain (root-mean-square deviation 0.45 A based on main-chain at

9 meric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 A) to each other as a co

10 class came despite nearly identical binding (root mean square deviation = 0.33 A) of these two compou

11 Benchmarking resulted in root mean square deviation = 1.78 kcal/mol and slope of

12 egree of conservation with protein kinase A (root mean square deviation = 1.8 A), indicating common a

13 and looks similar to Ca(2+) saturated GCAP1 (root mean square deviations = 2.0 A).

14 e-resolution three-dimensional models (helix root-mean-squared deviation, 5.7 A) of an adenine ribosw

15 The all-residue root mean square deviation about the average structure i

16 timized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (

17 d by the consensus chemical shift index, the root-mean-square deviation, amide 1H exchange rates and

18 component analysis, sequence alignments, and root mean-square deviation analysis corroborate the abov

19 Least-squares minimization, root-mean-square deviation analysis, and inspection of t

20 s, inter-residue contacts, sequence entropy, root mean square deviation and secondary structure and d

21 ubspace of the normal-mode vectors and using root mean square deviation as a test of accuracy, we fin

22 yclic voltammogram, and reproducibility with root mean square deviation as low as 1.3%.

23 ds in the case of Cartesian coordinate-based root-mean-square deviation as well.

24 l (KcsA), corresponding to a range of 2-30 A root mean-square deviations away from the native structu

25 structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A

26 structure quality measure of the coordinate root mean square deviation between a pair of structures

27 LC8 sequences show no identity, although the root mean square deviation between secondary structural

28 For individual subjects, the overall root mean square deviation between the model and DLW/DXA

29 The C-alpha root mean square deviations between a randomly chosen te

30 The mean root-mean-square deviation between equivalent C(alpha) a

31 The root-mean-square deviation between the theoretical and e

32 ough there was no apparent difference in the root-mean-square deviation between these two types of si

33 ious members of the ACAD family overlay with root-mean-square deviations between 1.7 and 3.1 A.

34 percent of the native contacts and that the root-mean-square deviations between contributing structu

35 thods are geometry based and make use of the root-mean-squared deviations between structures, while t

36 lution structure provided a approximately 3A root-mean-square deviation calculated from all the atoms

37 tory analysis capabilities including minimal root-mean-square-deviation calculations, secondary struc

38 As judged from the root mean-square deviations combined with the detailed s

39 minates between models better than Cartesian root-mean-square deviation (cRMSD).

40 the native state in C(alpha) distance-based root-mean-square deviation (dRMS) and C(beta) dRMS sense

41 Recently, we used distance-based root-mean-square deviation (dRMS) to compare the native

42 ns, decoys with 1.7- to 4.0-A all-heavy-atom root mean-square deviations emerge as those with the low

43 x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the

44 accuracy, with r(2) > 0.98 in all cases and root mean square deviation errors of <90 mV (mean absolu

45 ogous proteins mostly differ by less than 1A root mean square deviation, even when the sequence simil

46 GMO content between two extraction methods, root mean square deviation for kit is 0.208 and for CTAB

47 le of 30 structures with an average backbone root mean square deviation for residues 7-22 of 0.18 A f

48 The overall root mean square deviation for the structure was 1.15 A

49 yielded full-atom models that have 0.7-1.8 A root mean square deviations for the backbone atoms relat

50 The root mean squared deviation for the backbone atoms of th

51 ype MnSOD are nearly superimposable with the root mean-square deviation for 198 alpha-carbon atoms at

52 eins have very similar 3D structures, with a root-mean-square deviation for backbone atoms of 0.65 +/

53 The root-mean-square deviation for structured regions of the

54 ts (Ser1-Asn11 and Asp99-Met102), the atomic root-mean-square deviation for the 20 conformers with re

55 The experimental pairwise root-mean-square deviation for the measured 1JCalphaC' c

56 rgy conformers that differ in terms of their root-mean-square deviation, for a given radius of gyrati

57 ctive site in models having 3-4 A coordinate root mean square deviation from the native structure, a

58 For 20 computed structures, the root mean squared deviation from the average position of

59 n the aligned region of approximately 10% in root mean-square deviation from native over the initial

60 ies for selected point mutations, yielding a root-mean-square deviation from experimental results of

61 native-like topologies exhibit a coordinate root-mean-square deviation from native for the whole cha

62 mble native-like topologies whose coordinate root-mean-square deviation from native is between 3.0 A

63 f hydrogen bond constraints) with an average root-mean-square deviation from the mean coordinate posi

64 approach provides substantial improvement in root-mean-square deviation from the native structure ove

65 dues, a native-like structure, usually 4-6 A root-mean-square deviation from the native, is located.

66 ain is very stable: after 6 ns, the C(alpha) root-mean-square deviation from the starting structure i

67 Bond lengths and angles in the molecule have root-mean-square deviations from ideal values of 0.016 A

68 fuse with conformations exhibiting increased root-mean-square deviations from the experimental struct

69 in structure similarity is often measured by root mean squared deviation, global distance test score

70 y large conformational changes are observed (root mean square deviation >3 angstroms), using up to 10

71 The final model shows on average a root mean-square deviation improvement of 1.3, 1.3, and

72 al solubility data with calculated ones with root mean square deviations in the range of (0.08-1.55)%

73 5, PX65, and PX85, but for PX75 and PX95 the root mean-square deviation in coordinates exhibits large

74 The root mean-square deviation in coordinates with respect t

75 e equilibrium structure at 300 K, denoted as root-mean-square deviation in coordinates (CRMSD).

76 d as fragments of 30 residues or more with a root-mean-square deviation in superimposed alpha carbons

77 t of the X-ray structure of native PPDK (the root-mean-square deviation is 2.2 A).

78 ural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is unusually low for PBPs wi

79 low temperature simulations have a backbone root mean square deviation less than 2 A from the crysta

80 by using regression, root-mean-square error, root-mean-square deviation, Lin concordance correlation,

81 successfully predicts 42% of the cases with root mean square deviations lower than 1 A and 55% of th

82 ons lower than 1 A and 55% of the cases with root mean square deviations lower than 3 A.

83 ing functions range from 66% to 76% if using root-mean-square deviation < or =2.0 A as the criterion.

84 kinked conformations enables generating low-root mean square deviation models, and since then, we ha

85 that small values correlate with geometrical root mean square deviations obtained from structural ali

86 conformation that is practically identical (root mean square deviation of 0.154 A) to the recently i

87 f the inhibitor-free recombinant PLA2 with a root mean square deviation of 0.32 A for all the backbon

88 NMR structures were determined to a backbone root mean square deviation of 0.46 A and a heavy atom ro

89 geometries converged to an average pairwise root mean square deviation of 0.49 A.

90 e than 100 measured pKa values and yielded a root mean square deviation of 0.5 between calculated and

91 21 is extremely well defined with a backbone root mean square deviation of 0.52 A, thus forming a stu

92 structures are very similar with an average root mean square deviation of 0.5A for the Calpha atoms.

93 square deviation of 0.46 A and a heavy atom root mean square deviation of 0.93 A.

94 ransmembrane domains are well modeled (i.e., root mean square deviation of 0.94 A), whereas the loops

95 cases the final structural models lie within root mean square deviation of 1 approximately 2 angstrom

96 ermediate structural order having a backbone root mean square deviation of 1.04 A.

97 olated domain 1 could be superimposed with a root mean square deviation of 1.36 A for all backbone at

98 8-mer complex was determined with a backbone root mean square deviation of 1.46 A.

99 ty lipoprotein receptor (LB5), with backbone root mean square deviation of 1.5 A.

100 The final ensemble has an average pairwise root mean square deviation of 1.50 +/- 0.19 A taken over

101 ture shows localized conformational changes (root mean square deviation of 1.63 A), and its active si

102 ructurally ill-defined with a large backbone root mean square deviation of 1.91 A.

103 The core residues (18-41) overlay with a root mean square deviation of 2.29 +/- 0.62 A.

104 displays a unique level of asymmetry, with a root mean square deviation of 3.5A between all Calpha po

105 iled-coil structures are within 1-A C(alpha) root mean square deviation of a Crick-ideal backbone.

106 cture for the mutant hairpin with an average root mean square deviation of approximately 0.7 A for al

107 ipulation induces a distortion with a fitted root mean square deviation of coordinates (ignoring reti

108 verall structures superpose very well with a root mean square deviation of less than 1.6 A.

109 f the mutant C61A-C104A, which deviates by a root mean square deviation of more than 2.2 A from wild-

110 The lowest free-energy structure had a root mean square deviation of only 0.15 nm from native x

111 The root mean square deviation of the 69 ordered residues in

112 by SOAP-Loop is 1.5 A, close to the average root mean square deviation of the best sampled conformat

113 n the PLOP benchmark, the average main-chain root mean square deviation of the best scored conformati

114 The root mean square deviation of the ensemble of 20 refined

115 The root mean square deviation of the ensemble of 20 refined

116 The root mean square deviation of the main chain atoms in th

117 The root mean square deviation of the polypeptide backbone i

118 The root mean square deviation of the protein from its start

119 lecular dynamics calculations converged with root mean square deviations of 0.8-1.2 A for the R(12,2)

120 The average root mean square deviations of 20 structures calculated

121 otinamide binding proteins overlap well with root mean squared deviations of main chain atoms ranging

122 detail and the overall protein folds with a root mean-square deviation of <10 A.

123 high-solution NMR structure, with a backbone root mean-square deviation of 1.72 A (2JST), and the NMR

124 to their native structures, with an average root mean-square deviation of 4.99 A compared to the 5.3

125 hat at least one of its members would have a root mean-square deviation of no more than R A from any

126 (wt >/= 3)(cov) > 1.0 and > 0.4, the average root mean-square deviation of TASSER_WT (TASSER_2.0) mod

127 chain the set contains a conformation with a root mean-square deviation of, at most, R from the optim

128 enerated high-quality structural models with root mean-squared deviation of 1 approximately 3 A from

129 s true to the crystal form with a heavy atom root mean-squared deviation of 2 A.

130 mmetric unit with good stereochemistry and a root-mean-square deviation of 0.009 A and 1.63 from idea

131 forms of the enzyme are superimposed with a root-mean-square deviation of 0.36 A.

132 restraints and resulted in structures with a root-mean-square deviation of 0.40 +/- 0.05 A for backbo

133 ensemble has an average-to-the-mean backbone root-mean-square deviation of 0.50 A for the core four-h

134 is very similar to the NMR structure, with a root-mean-square deviation of 0.55 A for the main-chain

135 imer had favorable Ramachandran angles and a root-mean-square deviation of 0.59 +/- 0.13 A over super

136 ture for the loop-loop helix with an average root-mean-square deviation of 0.83 (+/-0.10) A for 33 co

137 Ca(2+)-loaded structure as evidenced by the root-mean-square deviation of 0.94 A for all backbone at

138 tures exhibited an average pairwise C(alpha) root-mean-square deviation of 0.98 A, and their stereoch

139 rmediates to within a defined limit--here, a root-mean-square deviation of 1 A.

140 but also for the absolute ones, which have a root-mean-square deviation of 1.0 kcal/mol (the maximum

141 y determined x-ray structure of HH26, with a root-mean-square deviation of 1.03 A.

142 hes the computational model, with a backbone root-mean-square deviation of 1.1 A.

143 stal structure of the Gln-GlnBP complex with root-mean-square deviation of 1.29 A.

144 ned solution structure, with a mean pairwise root-mean-square deviation of 1.33 A over the backbone h

145 ith the X-ray structure with a backbone atom root-mean-square deviation of 1.8 A.

146 ase (HPPD) in its closed conformation with a root-mean-square deviation of 1.85 A.

147 A root-mean-square deviation of 3.78 angstrom is observed

148 ith the native-state topology and an average root-mean-square deviation of 6 A from the native struct

149 ocrystalline ubiquitin has been refined to a root-mean-square deviation of about 1 A.

150 an 125 amino acids regularly have a backbone root-mean-square deviation of better than 5.0 A.

151 rigid body superposition that minimizes the root-mean-square deviation of C(alpha) atoms.

152 ured 2,3 A resolution crystal (structure the root-mean-square deviation of the 54 C(alpha) around the

153 The average root-mean-square deviation of the backbone atoms for the

154 The global root-mean-square deviation of the backbone atoms relativ

155 The root-mean-square deviation of the coordinates for the en

156 The root-mean-square deviation of the ensemble of 25 refined

157 The root-mean-square deviation of the ensemble of 28 refined

158 The backbone root-mean-square deviation of the ensemble of the calcul

159 TRV was quantified as 1.96 multiplied by the root-mean-square deviation of the fractional paired diff

160 The C(alpha) root-mean-square deviation of the model based on the rem

161 tional restraining potential is based on the root-mean-square deviation of the peptide coordinates re

162 ree of structural disruption, as measured by root-mean-square deviation of the predicted backbone str

163 semble of 19 rMD geometries showing pairwise root-mean-square deviations of <1.05 A.

164 ee R-factor of 28.3%, and good geometry with root-mean-square deviations of 0.013 A and 2.1 degrees f

165 The structure has root-mean-square deviations of 0.013 A from "ideal" bond

166 nts of variation < 1.0% and isotopic pattern root-mean-square deviations of 0.5-1.5%) while demonstra

167 cted structures, judged by comparison of the root-mean-square deviations of a room temperature ensemb

168 The lowest root-mean-square deviations of backbone atoms from the e

169 The average of the pairwise root-mean-square deviations of individual NMR conformers

170 high-quality structures, which had backbone root-mean-square deviations of less than 0.4 A.

171 ctures were of high quality and had backbone root-mean-square deviations of less than 0.5 A.

172 arkably similar and can be superimposed with root-mean-square deviations of not greater than 0.24 A.

173 The average of the pairwise root-mean-square deviations of the individual NMR confor

174 gned sequences can be folded with an average root-mean-square-deviation of 2.1 A to the target.

175 corresponding subunit of wild-type enolase (root-mean-squared deviation of 0.23 A).

176 nd structures that differ by a C(alpha)-atom root-mean-squared deviation of 7.1A.

177 The root-mean-squared deviations of the atoms lining the poc

178 of bound DNA was evaluated by calculating a root-mean-square deviation on fitting to a canonical B-D

179 The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with

180 he A and B forms of DNA agreed to a pairwise root mean square deviation (r.m.s.d.) of 1.04 +/- 0.3 A

181 are rebuilt and their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions an

182 framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions an

183 rises two beta-grasp folds having main chain root mean square deviation (r.m.s.d.) values from ubiqui

184 The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 A] was dete

185 e ensemble of 30 calculated structures has a root-mean-square deviation (r.m.s.d.) of 0.9 A, about th

186 The average of the root-mean-square deviations (r.m.s.d.) of the individual

187 close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 A.

188 he N- and C-terminal segments exhibit higher root mean square deviations, reflecting more flexibility

189 rced by a restraining potential based on the root mean-square deviation relative to the bound state c

190 a noticeable decrease in backbone coordinate root-mean-square deviation relative to the X-ray structu

191 s relative to the equatorial domain, and the root-mean-squared deviation relative to the r('') confor

192 es, resulting in an r(2) value of 0.70 and a root-mean-square deviation (rms) of 0.53 kcal/mol.

193 A simple root mean square deviation (RMSD) alignment of two diffe

194 for the chin was measured and reported using root mean square deviation (RMSD) and the Bland-Altman m

195 Initial root mean square deviation (RMSD) between the open and c

196 rently used in literature suffer from uneven root mean square deviation (RMSD) distribution with bias

197 Employing the relative root mean square deviation (RMSD) from native enables th

198 these methods yield models with at least 6 A root mean square deviation (RMSD) from the native struct

199 the experimental structure, with an average root mean square deviation (RMSD) of 2.2 A for the trans

200 l targets, MEDELLER gave an average backbone root mean square deviation (RMSD) of 2.62 A versus 3.16

201 precisely defined structure with an average root mean square deviation (RMSD) of approximately 1.2 A

202 lues and also reduces the overall side-chain root mean square deviation (rmsd) of the final model.

203 The average pairwise root mean square deviation (RMSD) over all 20 structures

204 rrelation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies

205 xist even in the decoys with a large overall root mean square deviation (RMSD) to the native.

206 d protein exhibits sub-A agreement [backbone root mean square deviation (rmsd)] with the computationa

207 tures using an algorithm that calculated the root mean squared deviation (rmsd) for the optimal super

208 Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 A for

209 The root mean squared deviation (RMSD) of the mean structure

210 es such as the correlation between score and root mean squared deviation (RMSD) to the native.

211 llowed side-chain flexibility and achieved a root mean-square deviation (RMSD) of 0.83 from experimen

212 ltidimensional scaling (MDS) of the pairwise root mean-squared deviation (RMSD) matrix of the conform

213 rally fall within 4 A of the native backbone root-mean square deviation (RMSD), despite the initial c

214 sual superposition, Levenshtein distance and root-mean-square deviation (RMSD) and are reasonably con

215 HDR of [ARAC] are similar to those in [OKA] (root-mean-square deviation (rmsd) approximately 0.8, 1.7

216 A weighted root-mean-square deviation (RMSD) between equivalenced g

217 The root-mean-square deviation (RMSd) between the two NMR st

218 Removing rotation by minimizing the root-mean-square deviation (RMSD) for the entire system

219 The overall backbone root-mean-square deviation (rmsd) for the structured por

220 023 (75%) proteins were folded to a C(alpha) root-mean-square deviation (RMSD) from native <6.5 A in

221 eproducibly obtained with a C alpha-backbone root-mean-square deviation (RMSD) from native of about 4

222 ues are within 0.6 ppm of experiment, with a root-mean-square deviation (RMSD) of 0.3 ppm.

223 le of 20 structures generated has an average root-mean-square deviation (RMSD) of 0.62 +/- 0.08 A for

224 n (residues 125-228), with a backbone atomic root-mean-square deviation (RMSD) of 0.67 A, consisting

225 E and dihedral restraints exhibit a backbone root-mean-square deviation (rmsd) of 0.77 A.

226 The root-mean-square deviation (rmsd) of 53 individual struc

227 fits were evaluated by the comparison of the root-mean-square deviation (rmsd) of calculated and meas

228 our threading program, PROSPECTOR_3, have a root-mean-square deviation (RMSD) to native < 6.5 angstr

229 e predicted within a factor of 6 (10 (0.78)) root-mean-square deviation (rmsd) using the CHARMM22 ele

230 highest scoring docked pose was within 2.5 A root-mean-square deviation (rmsd), with over 90% of the

231 Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbo

232 milar to those of native insulin (main-chain root-mean-square deviations (RMSD) of 0.45 and 0.54 A, r

233 The pairwise root-mean-square deviations (RMSD) of backbone N, Calpha

234 The root-mean-square-deviation (RMSD) after optimal superpos

235 ed from their respective binding sites using root-mean-squared deviation (rmsd) criteria.

236 deterioration of fit quality (as measured by root mean square deviation [RMSD] and residuals bitmap i

237 the molecules resemble one another closely (root mean square deviation [RMSD] C(alpha) = 1.5 A).

238 rated model closely matched (2.72-A C(alpha) root mean square deviation [RMSD]) the high-resolution (

239 n a two-dimensional(2D) plot upon structural root-mean-square deviations(RMSD) from either Dark or Li

240 nd close structural analogs, with an average root mean square deviation, RMSD, of 3 A and 87% alignme

241 nal states by clustering the models with low root-mean-square deviations (RMSDs).

242 gh-quality CDR H3 loops, the average minimum root mean square deviation sampled is 0.93 A, compared w

243 ICH is similar to human DJ-1 (1.6 A C-alpha root mean square deviation), structural differences in t

244 The 0.87-A root mean square deviation structure revealed a four-str

245 We exploit redundancy in PDB and, using root-mean-square deviation, study the conformational het

246 in Elk have significantly higher main-chain root-mean-square deviations than their counterparts in S

247 For example, helix A has much smaller root-mean-squared deviations than does helix D.

248 high-resolution structure, with the backbone root mean square deviation to the geometric average of t

249 formers representing the structure exhibit a root mean square deviation to the mean structure of 0.53

250 has been determined to high precision, with root mean square deviations to the mean structure of 0.3

251 ng a successful prediction as a model with a root mean-square deviation to native <6.5 A, the success

252 ial best template structures have an average root mean-square deviation to native of 5.3, 6.7, and 7.

253 e the CDR H1 and H2 loops exhibited a median root-mean-square deviation to natives of 3.1 and 1.5 A,

254 16, and 16-24 residue H3 loops with a median root-mean-square deviation to natives of 5.7, 4.5, and 6

255 for members of three families are within 1A root-mean-square deviation to the design models.

256 The resulting 20 conformers have an average root-mean-square deviation value relative to the mean co

257 mitochondrial matrix are less certain (i.e., root mean square deviation values of 0.72-2.06 A).

258 The root-mean-square deviation values for the 20 final struc

259 tting these regions from the comparison, the root mean squared deviation was 0.61 A (sigma = 0.13) fo

260 ates in the denatured state, pairwise Calpha root-mean-square deviations were measured between all st

261 refined structures was monitored by pairwise root-mean-square deviations which were <1.2 A; accuracy

262 refined structures was monitored by pairwise root mean square deviations. which were < 1.5 A; accurac

263 tingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimen

264 rge toward the native structure within 1-3 A root mean-square deviations with minimal computational c

265 The method achieves high accuracy, with root mean square deviations within 0.3 pH unit of the ex