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 orted lower deviations (ARD = -0.32 to 0.13; RMSD = 0.10 to 1.15).

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

4 ary RNA binding proteins (alignment 19-29aa, RMSD 1-1.5 Angstroms).

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

6 the crystallographic results to within 0.4A RMSD.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

38 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

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

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

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

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

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

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

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

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

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

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

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

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

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

52 (which assesses secondary structure), and an RMSD score (which measures overall rigidity).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

71 ng with hydrogen bond occupancy analysis and RMSD of the ligand in the pocket show CRA_1801 as the be

72 ilities, collision cross sections (CCS), and RMSD comparisons with values exceeding 26%.

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

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

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

76 Restraint violations and RMSD are poor measures of accuracy.

77 of L-chiral amino acids with a 1.0- angstrom RMSD to native enzyme active sites.

78 s and demonstrate an accuracy of ~3 angstrom RMSD(Calpha) against X-ray structures for sets of 15 to

79 leotide to, on average, within 3.63 angstrom RMSD of the experimental structure, while virtually remo

80 This initial model had 2.8- angstrom RMSD from the solution.

81 and experimentally validate a 2.98 angstrom RMSD irisin/alphaVbeta5 complex docking model.

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

83 raditional global similarity metrics such as RMSD or local similarity metrics such as changes in phi

84 and molecular dynamics simulations assessing RMSD, RMSF, and hydrogen bonds.

85 10 lowest energy structures have an all atom RMSD of 0.76 +/- 0.16 A.

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

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

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

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

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

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

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

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

94 0.09 +/- 0.12 A, and the backbone heavy-atom RMSD for the whole peptide is 0.96 +/- 2.45 A, the diffe

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

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

97 48 protein pairs, resulting in 2.2 A average RMSD for the predicted models, and only four cases in wh

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

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

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

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

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

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

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

105 loop structures, DeepH3 achieves an average RMSD of 2.2 +/- 1.1 angstrom on the Rosetta antibody ben

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

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

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

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

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

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

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

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

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

115 gets, respectively, and improved the average RMSD of predictions by 32.1% (1.4 angstrom).

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

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

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

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

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

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

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

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

124 estraints adopts conformations whose average RMSD is 5.44 A.

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

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

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

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

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

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

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

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

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

134 n 2.5 angstrom/5 angstrom interface backbone RMSD, with corresponding sampling in 81%/100% of the cas

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

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

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

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

139 f the TCR-pMHC complex, with a median Calpha RMSD of 2.31 angstrom.

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

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

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

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

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

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

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

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

148 table conformations, supported by consistent RMSD and RMSF values, compact structural organization (R

149 art of the complexes demonstrated consistent RMSDs, ranging from 3.57 to 3.64, with minimal residue f

150 nd-based measurements was highly consistent (RMSD = 0.66 mug m(-3)).

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

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

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

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

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

156 mize the overall root mean square deviation (RMSD) between the compared structures.

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

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

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

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

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

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

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

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

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

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

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

168 ieved an average root-mean-square deviation (RMSD) of 1.24 angstrom on a set of 50 experimental densi

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

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

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

172 y was defined as root mean square deviation (RMSD) of TD values at all 52 VF locations.

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

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

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

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

177 s, exhibited low Root Mean Square Deviation (RMSD) values, minimal Root Mean Square Fluctuation (RMSF

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

179 t a 2.2 angstrom root-mean-square deviation (RMSD).

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

181 es have a median root-mean-square-deviation (RMSD) of 2.39 angstrom to the true binding sites when st

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

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

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

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

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

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

188 (2.72-A C(alpha) root mean square deviation [RMSD]) the high-resolution (1.8-A) crystal structure of

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

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

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

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

193 ductions of the root-mean-square deviations (RMSDs) of the lowest scoring models.

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

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

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

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

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

199 res [measured by root-mean-squared distance (RMSD) from the experimental CDR H3 loop structure] than

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

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

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

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

204 nt violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore.

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

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

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

208 per makes predictions with an average CDR-H3 RMSD of 2.49 angstrom, which drops to 2.05 angstrom when

209 orrect folds for 260 proteins, where 28% had RMSDs below 2 angstrom.

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

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

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

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

214 ulations analysis, consistent fluctuation in RMSD and RMSF values, high Rg and hydrogen bonds in muta

215 the apo or holo states, but the increase in RMSD is less than 0.5 angstrom.

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

217 analyses, encompassing binding interactions, RMSD, RMSF, RoG, PCA, and FEL, were conducted to scrutin

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

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

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

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

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

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

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

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

226 e systems in which standard comparisons like RMSDs are difficult to compute.

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

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

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

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

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

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

233 models that scored well tended to have lower RMSDs.

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

235 ), the predicted binding sites have a median RMSD of 3.82 angstrom to the true binding sites.

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

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

238 of several popular model assessment methods (RMSD, TM-score, GDT, QCS, CAD-score, LDDT, SphereGrinder

239 y of the luteolin-SrtA complex, with minimal RMSD fluctuation and sustained hydrogen bonding througho

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

241 of these complexes, supported by analyses of RMSD, RMSF, hydrogen bonds, and MMGBSA free energy.

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

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

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

245 k and modified base pairs yielded an overall RMSD of 0.32 kcal/mol when compared with experimentally

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

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

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

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

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

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

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

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

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

255 identified previously by MDS of the pairwise RMSD matrix.

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

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

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

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

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

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

262 >19 restraints per residue are very similar (RMSD = 0.96 A).

263 odologies that are more advanced than simple RMSD are available but often require extensive mathemati

264 h both a low binding free energy and a small RMSD.

265 nd LPSO in finding both low-energy and small-RMSD docking conformations with high robustness in most

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

281 roducts to the ambimodal TS (measured by the RMSD) and the ratio of products formed in the dynamics s

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

283 -based rescoring, we matched or improved the RMSD of the best scoring model compared to Rosetta in 16

284 3 backbone N-H vectors slightly improved the RMSD values to 0.49 and 0.84 A, respectively.

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

286 enness with a continuous distribution in the RMSD space.

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

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

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

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

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

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

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

294 ng 173 simulated ridges, 115 can be tracked (RMSD < 0.001).

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

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

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

298 e compounds to MELK's ATP-binding site, with RMSD values <= 0.28 nm and compact structural dynamics (

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

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