ライフサイエンスコーパス: RMSD

1 RMSD calculations using a laptop CPU are 60x faster than

2 bone fold very similar to that of BAFF (1.1A RMSD over 122 structurally equivalent Calpha atoms), wit

3 Clustering analysis of the 2D RMSD distribution leads to 15 representative structures

4 the crystallographic results to within 0.4A RMSD.

5 ed to the observed geometries to within 0.7A RMSD or better.

6 *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures.

7 ull atomic structures that are within 1.00 A RMSD of the starting structure.

8 s in most enzymes is very small (usually 1 A RMSD between the apo and substrate-bound forms across th

9 he predicted orientation is very close (<1 A RMSD) to the crystallographically observed orientation i

10 close to that of the in silico model (1.1 A RMSD) while it differs significantly from that of wild-t

11 large hinge-bending-type motions with 4-12 A RMSD (root mean-square distance) between open and closed

12 istent with the close correspondence, 0.16 A RMSD for regions of secondary structure and 0.51 A RMSD

13 gand pose is correctly positioned within 2 A RMSD for 64% (54/85) of cases overall.

14 rom crystal structures to within 1.87-3.31 A RMSD of the full atomic crystal structure.

15 in length with atomic-level accuracy (<1.5 A RMSD).

16 or regions of secondary structure and 0.51 A RMSD overall, for the crystal structure of free ecTbetaR

17 ntical amino acid residues are within 0.55 A RMSD of the comparable structure in the FixJ receiver, a

18 A threshold of 0.67 A RMSD for all atoms of corresponding residues ensures inc

19 gn in three dimensions rather poorly (4.85 A RMSD; Z-score, 8.58).

20 (with initial 4.1-7.1 A and final 1.7-2.9 A RMSD to target).

21 solated rabbit Cd(4)-alpha was measured at a RMSD of 2.0 A.

22 n hit proteins can give 90% coverage below a RMSD of 3.5A for proteins up to 320 residues long.

23 odel excluding the two charged ligands had a RMSD of 0.87 kcal/mol.

24 nity model for the full set of ligands had a RMSD of 1.10 kcal/mol.

25 est of the top five full-length models has a RMSD < 6.5 angstroms.

26 tein G, the lowest energy conformation has a RMSD of 2.62 A for the three extracellular interacting l

27 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster cen

28 ately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centr

29 raints, 1206 (88%) proteins were folded to a RMSD <6.5 A and the average RMSD improved to 4.1 A.

30 restraints and 61 proteins were folded to a RMSD <6.5 A with N/4 restraints.

31 ved restraints, 47 proteins were folded to a RMSD <6.5 A with N/8 restraints and 61 proteins were fol

32 ve 60% coverage by a template protein with a RMSD below 3.5A and 6.0% have 70% coverage.

33 h average sequence identity of 9.8%), with a RMSD less than 4A, and 79% average coverage.

34 ed) were predicted with reasonable accuracy (RMSD of 0.49 A and 1.07 A) even though no corresponding

35 tiple trajectories, with the lowest C(alpha) RMSD being 0.39 A for residues 2-34 (excluding residues

36 formational family, with an average C(alpha) RMSD of 1.3 A for S15 and 1.2 A for HP-36 core (1.9 A ov

37 ter of most populated cluster had a C(alpha) RMSD of 1.63 A.

38 within approximately 35 ps and 3 A C(alpha) RMSD of the transition state ensemble identified in a pr

39 ee energies also contained the best C(alpha) RMSD structures (1.4 A for S15 and HP-36 core) and the l

40 while the best possible model has a C(alpha) RMSD value of 5.3A.

41 o that of human DJ-1 (0.9 angstroms C(alpha) RMSD) and both proteins adopt the same dimeric structure

42 nd were quite similar (within 3.5 A C(alpha) RMSD).

43 lpha) atoms between two structures (C(alpha) RMSD)=0.2 A], and the active-site residues are superposa

44 and rat proteins are very similar (C(alpha) RMSD=0.4 A), several nonconserved residues are present i

45 HP-36 core) and the lowest average C(alpha) RMSDs (1.8 A for S15, 2.1 A for HP-36 core).

46 s)) correlate well with the average C(alpha) RMSDs (r(s) = 0.77 for HP-36, r(s) = 0.83 for S15).

47 osetta models were nearly all <2.5 A C(alpha)RMSD from the experimental structure; this result demons

48 A) free energies and alpha carbon (C(alpha)) RMSDs were then calculated for each family.

49 ins and that acceptable models (with C alpha-RMSD values to the native of 2 A or less in the transmem

50 the structure and all the cores built had an RMSD of 3.7 A or less to the target structure.

51 he three lowest energy template loops had an RMSD of less than 1.79 A.

52 cted for the first designed sequence have an RMSD of <2 A to the target structure in 62% of cases.

53 9), the resultant full-length models have an RMSD to native below 6 A (97% of them below 4 A).

54 he analogous normal structure resulted in an RMSD of 0.53 A over all atoms.

55 ut of 18) loops of up to nine residues to an RMSD better than 1.07 A relative to the crystal structur

56 al structure with precision equivalent to an RMSD of 0.4 A.

57 RalB bound to the GTP analogue GMPPNP to an RMSD of 0.6 A.

58 ugh the structures are very similar, with an RMSD in backbone atom positions of 1.4 A when loop regio

59 e chains, is extremely well-defined, with an RMSD of 0.54 A.

60 d disulfide has been obtained by NMR with an RMSD of 0.56 A for all the backbone atoms of the protein

61 tructure was approached successfully with an RMSD of 0.9-4.1 A when a relatively low cutoff radius of

62 esponding inhibitor complexes of PR1 with an RMSD of 1.1 A on main-chain atoms.

63 lated structure matched the original with an RMSD of 1.24 A.

64 ot identical with, the design model, with an RMSD of 1.4 A over active-site residues and equivalent s

65 ictor is able to reproduce distances with an RMSD of 6A, regardless of the evolutionary content provi

66 etermined by X-ray fiber diffraction with an RMSD value of 2.0 A.

67 DT_TS (at least +2.6, p-values < 0.0005) and RMSD (-0.4, p-values < 0.005).

68 group consistently had the lowest energy and RMSD values, consistent with an X-ray analysis of the sa

69 confidence score, the estimated TM-score and RMSD, and the standard deviation of the estimations.

70 or calculating the optimal superposition and RMSD that is designed for parallel applications.

71 The statistical significance of any RMSD is assigned by reference to a distribution fitted t

72 10 lowest energy structures have an all atom RMSD of 0.76 +/- 0.16 A.

73 goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms.

74 Our predictions are within ~2.7 A all-atom RMSD of the respective crystal structures of the ancestr

75 o within 0.20 A backbone and 0.33 A all-atom RMSD.

76 o within 0.28 A backbone and 0.42 A all-atom RMSD; a model refined against the average simulation den

77 NA structure and the 2:1 complex (heavy atom RMSD 1.55 A) reveal that these sequence-dependent featur

78 ved via NMR spectroscopy (protein heavy atom RMSD approximately 0.93 +/- 0.12 A).

79 consistent with a higher backbone heavy atom RMSD of approximately 1.22 A (vs 0.84 A overall) between

80 The backbone heavy-atom RMSD for residues L14 through M21 is 0.09 +/- 0.12 A, an

81 0.09 +/- 0.12 A, and the backbone heavy-atom RMSD for the whole peptide is 0.96 +/- 2.45 A, the diffe

82 To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of res

83 ly determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 A.

84 48 protein pairs, resulting in 2.2 A average RMSD for the predicted models, and only four cases in wh

85 r the binding site region is 0.57 A (average RMSD from the mean: 0.39 A).

86 ration being highly expanded with an average RMSD > or = 10 A.

87 lations of our test set result in an average RMSD from native of 3.7 A and this further reduces to 2.

88 identical to the targets, giving an average RMSD of 0.5A.

89 d obtain a well-defined loop with an average RMSD of 1.1 A for the loop nucleotides of 11 converged s

90 finities, and predicted poses had an average RMSD of 1.7A to the crystallographic poses.

91 Our method achieves an average RMSD of 1.93 A for lowest energy conformations of 36 pai

92 to reconstruct the targets within an average RMSD of 2A.After demonstrating the reconstruction potent

93 forms from our simulations reach an average RMSD of 3.6 A from the target forms, closely matching th

94 ast one near-native complex, with an average RMSD of 5 A from the native structure.

95 docking for these 21 cases yields an average RMSD of 5.5 A.

96 Overhauser effects (NOEs) and has an average RMSD to the mean structure of 0.25 A for the backbone an

97 ensemble of the native basin has an average RMSD value of 4 A from the native structure.

98 ence similarity, for a small cost in average RMSD.

99 ure prediction for a number of RNAs (average RMSD of 2.93 A) and the sequence-specific variation of f

100 were folded to a RMSD <6.5 A and the average RMSD improved to 4.1 A.

101 ct docked complexes and to lower the average RMSD of the best-scoring docked poses relative to the ri

102 target proteins with four loops, the average RMSD of the lowest energy conformations is 2.35 A.

103 The average RMSD of the models for all 1365 proteins is 5.0 A.

104 The average RMSD of the predicted pose to the experiment was 2.0 A (

105 For the rigidly packed residues, the average RMSD to the mean structure is 0.57 A for the backbone at

106 M-score, and GDT-HA score, while the average RMSD was improved by a new sampling approach.

107 has been folded to structures whose average RMSD from native is 5.65 A.

108 has been folded to structures whose average RMSD is 4.28 A.

109 estraints adopts conformations whose average RMSD is 5.44 A.

110 nsport membrane protein MerF with a backbone RMSD of 0.58 A.

111 rmation from F9 through R27, with a backbone RMSD of 0.65 A and a side chain RMSD of 1.66 A.

112 ociation with MMP-3, evident from a backbone RMSD of 1.15 A.

113 predicts structures to within 1-2 A backbone RMSD relative to X-ray and NMR structures.

114 structure of one design had a 0.8 A backbone RMSD to the computational model in the rebuilt region.

115 ieves an average accuracy of 0.93 A backbone RMSD versus 1.56 A for Modeller.

116 cular models of high accuracy (<3 A backbone RMSD) from models of lower accuracy (>4 A backbone RMSD)

117 from models of lower accuracy (>4 A backbone RMSD).

118 The average minimum global backbone RMSD for 1,000 conformations of 12-residue loops is 1:53

119 nce between the two scFv molecules (backbone RMSD of 0.6A), despite the large difference in affinity.

120 The backbone RMSD to the geometric average for 19 final structures is

121 of four peptides determined to <1 A backbone RMSDs, allowing direct comparison of thermodynamic stabi

122 pts a conformation that is within 1-A Calpha RMSD of the computational model.

123 ndant pMHC-I structures from the PDB (Calpha RMSD below 1 A).

124 ries within a given time window) with Calpha RMSD values from the native structure less than 5 A (fra

125 rgy structure at 300 K is only 1.50 A Calpha-RMSD (Calpha-rms deviation) from the NMR structures.

126 inversion of A2 orientation (core side chain RMSD 0.75 A excluding A2); in the T-state, allo-Ile(A2)

127 h a backbone RMSD of 0.65 A and a side chain RMSD of 1.66 A.

128 organization of the surrounding side chains (RMSD 0.98 A).

129 to the well-characterized TrxR from E. coli (RMSD 1.30 A (2) for chain A), the "NADPH binding pocket"

130 nding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked

131 lds to native with an average rms deviation (RMSD) from native of 2.5 A with approximately 82% alignm

132 A simple root mean square deviation (RMSD) alignment of two different conformations of the sa

133 ein distance and root-mean-square deviation (RMSD) and are reasonably consistent with related search

134 d reported using root mean square deviation (RMSD) and the Bland-Altman method.

135 A weighted root-mean-square deviation (RMSD) between equivalenced groups of amino acids is used

136 Initial root mean square deviation (RMSD) between the open and closed forms of the subunit i

137 ffer from uneven root mean square deviation (RMSD) distribution with bias to non-protein like hydroge

138 y minimizing the root-mean-square deviation (RMSD) for the entire system is found to be more appropri

139 ed to a C(alpha) root-mean-square deviation (RMSD) from native <6.5 A in one of the top five models.

140 ing the relative root mean square deviation (RMSD) from native enables the assessment of the statisti

141 C alpha-backbone root-mean-square deviation (RMSD) from native of about 4. A.

142 ith at least 6 A root mean square deviation (RMSD) from the native structure.

143 periment, with a root-mean-square deviation (RMSD) of 0.3 ppm.

144 d has an average root-mean-square deviation (RMSD) of 0.62 +/- 0.08 A for backbone (N, Calpha, C) ato

145 backbone atomic root-mean-square deviation (RMSD) of 0.67 A, consisting of three alpha-helices (resi

146 y and achieved a root mean-square deviation (RMSD) of 0.83 from experimental values (0.68 after disco

147 with an average root mean square deviation (RMSD) of 2.2 A for the transmembrane region and 5 A for

148 average backbone root mean square deviation (RMSD) of 2.62 A versus 3.16 A for Modeller.

149 with an average root mean square deviation (RMSD) of approximately 1.2 A for the entire molecule.

150 average pairwise root mean square deviation (RMSD) over all 20 structures for the binding site region

151 PECTOR_3, have a root-mean-square deviation (RMSD) to native < 6.5 angstroms, with >70% alignment cov

152 coys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap

153 a large overall root mean square deviation (RMSD) to the native.

154 native backbone root-mean square deviation (RMSD), despite the initial configuration being highly ex

155 The root-mean-square-deviation (RMSD) after optimal superposition is the predominant mea

156 ks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 A for 8 and 12 residues loops, resp

157 of the pairwise root mean-squared deviation (RMSD) matrix of the conformations sampled in a thermal u

158 The root mean squared deviation (RMSD) of the mean structure is 0.53 A for main-chain ato

159 tween score and root mean squared deviation (RMSD) to the native.

160 (as measured by root mean square deviation [RMSD] and residuals bitmap images).

161 another closely (root mean square deviation [RMSD] C(alpha) = 1.5 A).

162 (2.72-A C(alpha) root mean square deviation [RMSD]) the high-resolution (1.8-A) crystal structure of

163 with an average root mean square deviation, RMSD, of 3 A and 87% alignment coverage.

164 tzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect t

165 lin (main-chain root-mean-square deviations (RMSD) of 0.45 and 0.54 A, respectively), differences in

166 The pairwise root-mean-square deviations (RMSD) of backbone N, Calpha, and C' atoms for the second

167 models with low root-mean-square deviations (RMSDs).

168 are within 2-5 A root mean squre deviations (RMSDs) from corresponding experimentally derived structu

169 upon structural root-mean-square deviations(RMSD) from either Dark or Light state.

170 folds with an root-mean-square displacement (RMSD) of approximately 0.5 A.

171 rence between the Root Mean Square Distance (RMSD) from canonical A-form and B-form DNA is used as an

172 finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching

173 ptides, including the E-selectin EGF domain (RMSD approximately 1.08 A).

174 cal in both EF-hand calcium-binding domains (RMSD=0.19).

175 ops is 1:53 A degrees , with a lowest energy RMSD of 2:99 A degrees , and an average ensembleRMSD of

176 erage error of 0.08 for TM-score and 2 A for RMSD.

177 However, global RMSD is dependent on the length of the protein and can b

178 cture similarity measure, such as the global RMSD, the quality of models for multiple chain complexes

179 gned protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 A respectively

180 dicted and experimental structures was high (RMSD between 1.2 and 1.4 A), whereas for another 2, the

181 ource, including the GPU code and the hybrid RMSD subroutine, can be downloaded and used without rest

182 We observed a decrease in RMSD in comparing the final average RNA structures and i

183 cid sequence can lead to a rapid decrease in RMSD to native due to incorrect packing.

184 as lower but retained most key interactions (RMSD 2.4-2.6 A).

185 anked pHDock structures have lower interface RMSDs and recover more native interface residue-residue

186 Main-chain atoms in these regions show large RMSD values in the average NMR structure.

187 For the experimental group, the largest RMSDs were 1.1 mm in anteroposterior direction and 2.6 d

188 control group without templates, the largest RMSDs were 2.63 mm in superoinferior direction and 7.21

189 roMOL, including the expanded motif library, RMSD calculations and output selection formatting, have

190 The average ligand RMSD for docking to a flexible receptor for the 21 pairs

191 wed by docking, generating an average ligand RMSD that is 1-2 A better than docking with homology mod

192 elling quality across 82 targets, the ligand RMSD with respect to the experimental structure is 1.4 A

193 of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphi

194 )-(Cm(32),Gm(34), m(1)G(37),m(5)C(40)) (loop RMSD 0.98A) exhibited a significantly restricted conform

195 of ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)) (loop RMSD 2.58A).

196 Despite a 83% sequence homology and a low RMSD for the backbone heavy atoms (0.648 A) in the cryst

197 uced in the simulation is large, so that low RMSD structures are not generated starting from an unfol

198 ulting library contained structures with low RMSD versus the native structure.

199 he best loops with an 8% improvement by mean RMSD compared to the loops generated by Builder.

200 tion of 20 antibodies with an average/median RMSD of 2.1/1.6 A to the crystal structures.

201 time, this approach maintains a small median RMSD from the leading all-atom approach (as measured in

202 The mean model RMSD generated from 3D-Coffee using multiple templates i

203 New GPU code further increases the speed of RMSD and TM-score calculations.

204 ility including: 2D-scaling visualization of RMSD distances between structures of the same protein, g

205 lped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%

206 ions in a few cases, resulting in an overall RMSD of 0.85 pH units.

207 f backbone flexibility increased the overall RMSD to 0.93 pH units but improved relative pK(a) predic

208 nd 108M structures are very similar overall [RMSD of C(alpha) atoms between two structures (C(alpha)

209 d the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0A) as fpair and pr

210 iolations greater than 0.13 A and a pairwise RMSD over the binding site of 0.80 A.

211 mbles of 20 conformers with average pairwise RMSD values of 0.46, 0.52, and 0.62 A from their mean st

212 d at different sites in the groove (pairwise RMSD 4.3-12.6 A) we arrive at three very similar structu

213 The mean pairwise RMSD of the secondary structural elements was 0.63 A for

214 e at three very similar structures (pairwise RMSD 0.80-1.34 A) representing one converged binding sit

215 identified previously by MDS of the pairwise RMSD matrix.

216 well-converged, with backbone atom position RMSDs of 0.21 A for the main body of the peptide between

217 the uncertainty corresponds to a positional RMSD of 0.17 A.

218 proteins, with one-third having a predicted RMSD < 5.5 A.

219 ps, simulation trajectories, gyration radii, RMSDs from native state, fraction of native-like contact

220 for each of the training pairs are similar (RMSD< approximately 4A) but the sequence relationship is

221 which the pair-wise structures are similar (RMSD< approximately 4A) but the sequences are marginally

222 >19 restraints per residue are very similar (RMSD = 0.96 A).

223 ASL structures had similarly resolved stems (RMSD approximately 0.6A) of five canonical base-pairs in

224 idelity with the crystallographic structure (RMSDs 0.29 and 0.34 A, respectively).

225 are well defined in the solution structures (RMSD = 0.59 A) and are consistent with previously determ

226 quare Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics.

227 domonas sp. CF600 phenol hydroxylase system (RMSD = 2.48 A for backbone atoms), that of MMOB reveals

228 calculations are, however, much slower than RMSD calculations.

229 The RMSD of backbone atoms for the ensemble of 33 structures

230 The RMSD of the 15 lowest energy structures was 0.68 A, indi

231 The RMSD of the backbone structure (Q15-A42) is 0.71 +/- 0.1

232 The RMSD of the NMR conformers (residues 13-80) is 0.37 A fo

233 The RMSD of the NMR conformers for residues 2-92 excluding r

234 ible receptor for the 21 pairs is 1.4 A; the RMSD is < or =1.8 A for 18 of the cases.

235 for the precursor amino acid, and so are the RMSD values for the atoms shared with the precursor amin

236 On average, the RMSD of full-length models is 2.25 A, with aligned regio

237 those for which the correlation between the RMSD and the scoring function were highest.

238 ditional information over just comparing the RMSD of static structures.

239 3 backbone N-H vectors slightly improved the RMSD values to 0.49 and 0.84 A, respectively.

240 bound conformations found improvement in the RMSD of side-chains in the interface of protease-inhibit

241 enness with a continuous distribution in the RMSD space.

242 For 6 of 14 predictions, the RMSD is <5.0 A, with a GDT_TS score greater than 60.0.

243 We find that the RMSD from native is highly dependent on the accuracy of

244 found to be more appropriate than using the RMSD for only the more rigid part of the system.

245 ted models, and only four cases in which the RMSD exceeded 3 A.

246 es produced are very well converged with the RMSD of backbone atom positions of the main body of the

247 The RMSDs of the 20 X-PLOR-generated structures were 0.71 +/

248 shown to have similar 3-D structures through RMSD analysis of the RNA structural constituents.

249 ng protocol to generate potential energy vs. RMSD landscapes.

250 atomic coordinates using a Gaussian-weighted RMSD (wRMSD) fit.

251 ary structure of transmembrane segments with RMSD <6.0 A for 9 of 14 proteins.

252 For the three cases with RMSDs greater than 1.8 A, the core of the ligand is prop

253 backbone conformations that superimpose with RMSDs of 1.0 A over the regions of regular secondary str