ライフサイエンスコーパス: backbone atom

1 identical conformations (rmsd of 0.27 A for backbone atoms).

2 ely governed by residues positioning the Trp backbone atoms.

3 gives an overall r.m.s.d. of 1.09 A for the backbone atoms.

4 r moieties within single residues, including backbone atoms.

5 sd difference of only 1.37 A, when comparing backbone atoms.

6 mean square deviation of 0.32 A for all the backbone atoms.

7 tal structure with an rmsd of 1.52 A for the backbone atoms.

8 hibitors via hydrogen bonding to nonreactive backbone atoms.

9 molecular mimicry, and interactions with RBM backbone atoms.

10 of the interaction of the side chain to the backbone atoms.

11 s eliminated by artificially discharging the backbone atoms.

12 root-mean-square deviation of 0.94 A for all backbone atoms.

13 tial dynamic properties of side-chain versus backbone atoms.

14 in little, or no, change in the position of backbone atoms.

15 , and thus is presumably mediated by peptide backbone atoms.

16 close in sequence (<+/-4), mainly involving backbone atoms.

17 d of 0.47 A from the mean structure for core backbone atoms.

18 nguishable from that observed previously for backbone atoms (0.93 +/- 0.03).

19 egree of structural similarity between their backbone atoms (0.96-A root mean square deviation).

20 the 30 structures is 0.37 +/- 0.04 A for the backbone atoms, 0.78 +/- 0.05 A for all atoms, and 0.45

21 7-137 and 145-163 is 0.42 +/- 0.04 A for the backbone atoms, 0.80 +/- 0.04 A for all atoms, and 0.50

22 the 30 structures is 0.43(+/-0.05) A for the backbone atoms, 0.80(+/-0.09) A for all atoms, and 0.47(

23 r residues 29-152 is 0.43 +/- 0.03 A for the backbone atoms, 0.83 +/- 0.05 A for all atoms, and 0.51

24 the 30 structures is 0.47 +/- 0.05 A for the backbone atoms, 0.86 +/- 0.05 A for all atoms, and 0.56

25 ared deviation was 0.61 A (sigma = 0.13) for backbone atoms, 0.86 A (sigma = 0.12) for all associated

26 PBPs, although the structural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is

27 toxin has an average rmsd of 0.89 A for the backbone atoms among 38 converged conformers.

28 derived from them is 0.74 +/- 0.26 A for all backbone atoms and 0.49 +/- 0.22 A when residues Pro(14)

29 aving an average rmsd of 0.42 +/- 0.08 A for backbone atoms and 0.71 +/- 0.07 A for heavy atoms to th

30 egion reduces overall the rmsd to 0.30 A for backbone atoms and 0.71 A for all heavy atoms.

31 root-mean-square precision of 0.38 A for the backbone atoms and 0.76 A for all atoms in the beta-sand

32 uding residues 37-45 and 64-73 is 0.41 A for backbone atoms and 0.88 A for all heavy atoms.

33 2, 81, and 82 was 0.52 A (sigma = 0.096) for backbone atoms and 0.90 A (sigma = 0.122) for all heavy

34 viations to the mean structure of 0.38 A for backbone atoms and 0.94 A for all heavy atoms of ordered

35 RMSD to the mean structure is 0.57 A for the backbone atoms and 1.00 A for all heavy atoms.

36 ealing structures is 0.79 +/- 0.18 A for the backbone atoms and 1.06 +/- 0.15 A for all atoms.

37 secondary structure region is 0.40 A for the backbone atoms and 1.09 A for all atoms.

38 emble of structures is 0.55( +/- 0.09) A for backbone atoms and 1.10( +/- 0.08) A for all heavy atoms

39 mposed to the average is 0.73 +/- 0.10 A for backbone atoms and 1.42 +/- 0.16 A for heavy atoms.

40 5 and 127-138), RMS deviations are 1.1 A for backbone atoms and 1.6 A for all non-hydrogen atoms.

41 as 0.54 +/- 0.18 and 0.92 +/- 0.20 A for the backbone atoms and all heavy atoms, respectively, of all

42 as 0.54 +/- 0.26 and 0.98 +/- 0.23 A for the backbone atoms and all heavy atoms, respectively.

43 0.57 +/- 0.14 A and 1.11 +/- 0.19 A for the backbone atoms and all heavy atoms, respectively.

44 ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial

45 istance deviation of 0.51 and 0.95 A for the backbone atoms and for the non-hydrogen atoms, respectiv

46 e connected by a tunnel lined primarily with backbone atoms and hydrophobic and nonpolar amino acid r

47 frequently on the involvement of the protein backbone atoms and metal ion cofactors.

48 atbelt loop and the LHR, if any, involve its backbone atoms and possibly the side chain of residue be

49 ns-whether pore-facing or buried-rather than backbone atoms and propose a mechanism whereby not only

50 , backbone modifications alter the number of backbone atoms and the identities of backbone atoms rela

51 f 0.9 A, about the average structure for the backbone atoms, and 1.2 A for all heavy-atoms of the dim

52 the relative orientation of the constituent backbone atoms, and generate structures by denoising fro

53 ential NOE cross-peaks, and S2 values of the backbone atoms, and the conserved side-chain dynamics of

54 is phenomenon and that the electrostatics of backbone atoms are not critically involved.

55 This unnatural hexad has the same number of backbone atoms as a heptad of alpha residues.

56 -long coat protein, including 136 of the 138 backbone atoms, by means of two- and three-dimensional 1

57 These amino acids all bind with their backbone atoms close to the active-site zinc ion and the

58 owed by graph networks that directly predict backbone atom coordinates.

59 g the branch point primarily through peptide backbone atoms enables processing of diverse tubulin iso

60 The RMSD of backbone atoms for the ensemble of 33 structures relativ

61 he average root-mean-square deviation of the backbone atoms for the final 24 structures relative to t

62 The average RMS deviation of the backbone atoms for the final 25 structures relative to t

63 The superposition of the active site backbone atoms for the high-quality and minimal restrain

64 violations exhibited low rms deviations for backbone atoms for the overwhelming majority of the resi

65 mean rmsd from the average structure for all backbone atoms from residues 6-205 in the best 21 calcul

66 The lowest root-mean-square deviations of backbone atoms from the experimentally determined struct

67 eometric functions of the coordinates of the backbone atoms from the protein chains.

68 For NADP+-complexed MurB, one or more backbone atoms have been assigned for 313 residues (90%)

69 the case of substrate-free MurB, one or more backbone atoms have been assigned for 334 residues (96%)

70 loops is 0.57(+/-0.10) A while the rmsd for backbone atoms in beta-strands is 0.45(+/-0.08) A.

71 Nevertheless, backbone atoms in core catalytic site residues Ser64, Ly

72 tal uncertainty are of similar magnitude for backbone atoms in even high-resolution structures, so co

73 ubunit cystine knot and the tensor loop with backbone atoms in loop alpha2, a process that causes the

74 ic evidence of specific desolvation of helix backbone atoms in model alanine-rich peptides.

75 binding led to changes in chemical shifts of backbone atoms in residues Arg233 and Phe234 of loop 3 (

76 The beta/gamma diad retains the number of backbone atoms in the alphaalphaalpha triad.

77 about the mean coordinate is 0.46 A for the backbone atoms in the highly structured region and 0.88

78 tural homologs and was only resolved for the backbone atoms in the initial vSGLT structure (Protein D

79 ed in several critical interactions with the backbone atoms in the S1' and S2 subsites of HIV-1 prote

80 e chains but with well-separated ends of the backbone atoms in the VGSN turn.

81 The assigned backbone atoms include 309 1HN and 15N atoms (94%), 315

82 The chemical shifts of the backbone atoms indicate that the coat protein conformati

83 Interactions of the nicotinic acid with backbone atoms indicate the structural basis for specifi

84 With only backbone atoms information, ICOSA is at least comparable

85 dues), mainly because of a better packing of backbone atoms into the framework of the antibody model.

86 r35 with Gly greatly increases the number of backbone atoms involved in such motions.

87 the positioning of hydrogens relative to the backbone atoms is one of the factors limiting the accura

88 The r.m.s.d. over all of the 118 residues (backbone atoms) is 0.73 A.

89 rogen bond satisfaction is attractive: polar backbone atoms must form hydrogen bonds, either intramol

90 ers relative to the mean coordinates for the backbone atoms N, C(alpha) and C' of residues 5 to 68 is

91 their mean structures, respectively, for the backbone atoms N, C(alpha), and C' of residues 2-11.

92 ers relative to the mean coordinates for the backbone atoms N, C2 and C' of residues 4 to 54 and 4 to

93 s, relative to the mean coordinates, for the backbone atoms N, Calpha and C' of residues Phe5 through

94 o the mean coordinates of 0.54 A for all the backbone atoms N, Calpha and C', and of 1.01 A for all h

95 sd of 0.44 A from the mean structure for the backbone atoms N, Calpha, and C' of residues 2-11.

96 ue to increased solvent accessibility of the backbone atoms near the smaller Cys.

97 An analysis of backbone atom NMR chemical shift changes and backbone am

98 s well-defined with a rms difference for the backbone atoms of 0.27 +/- 0.06 A.

99 tures, with a root-mean-square deviation for backbone atoms of 0.65 +/- 0.13 A2.

100 have a root-mean-square difference over the backbone atoms of 0.97 A).

101 iation of 3.78 angstrom is observed over the backbone atoms of 36 equivalent helical positions.

102 rithm, geometric hashing, to superimpose the backbone atoms of a given pair of interfaces, and provid

103 d strong hydrogen bond interactions with the backbone atoms of active-site amino acid residues (Asp29

104 eraction between heparin/heparan sulfate and backbone atoms of FGF19/23.

105 ibitor interacts with the side chains and/or backbone atoms of Lys-53, Ser-55, Thr-56, Arg-57, Thr-58

106 ar 2'-OH and 3'-OH groups hydrogen bonded to backbone atoms of Nuc.

107 ion of an intermediate species, in which the backbone atoms of residues 65-67 have condensed to form

108 to increase H-bonding interactions with the backbone atoms of residues Asp 29, Asp 30, and Gly 48 le

109 to the calculated average structure for the backbone atoms of residues excluding the N terminus and

110 SKT05 bound backbone atoms of sequence-diverse residues, enabling br

111 unit and intrasubunit hydrogen bonds between backbone atoms of several residues in the beta-subunit c

112 mean-square deviation of 0.40 +/- 0.05 A for backbone atoms of superimposed secondary structural elem

113 We have assigned the chemical shifts of the backbone atoms of the 32 kDa ligand-binding domain of PP

114 The rmsd for the backbone atoms of the A form is 0.54 A (0.92 A for all n

115 actions from 1 aa side chain and polypeptide backbone atoms of the antibody light and heavy chains.

116 mits the formation of hydrogen bonds between backbone atoms of the beta-subunit cystine knot and the

117 sitive to hydrogen-bonding interactions with backbone atoms of the DNA.

118 Surprisingly, while the backbone atoms of the F helix have higher rmsds and larg

119 In the DNA free state the backbone atoms of the helix-turn-helix motif are general

120 ogen bonding interactions with both base and backbone atoms of the host RNA.

121 eceptors form a 'charge clamp' that contacts backbone atoms of the LXXLL helices of SRC-1.

122 ed by NMR with an RMSD of 0.56 A for all the backbone atoms of the protein and the well-defined porti

123 t superimpose with an rmsd of 0.71 A for the backbone atoms of the structured regions.

124 The root mean squared deviation for the backbone atoms of the two transmembrane helices was 0.63

125 terminal Gly of the alpha-chain, and peptide backbone atoms of two aromatic residues.

126 In the catalytic complex, the polar backbone atoms of two symmetry-related I68 residues prov

127 adenines via base-specific interactions with backbone atoms, offering a molecular basis for TA target

128 e strength of hydrogen bond networks between backbone atoms on different chains depends on the local

129 uivalent atoms was 0.84 A (sigma = 0.12) for backbone atoms over all residues.

130 The structures are well-converged, with backbone atom position RMSDs of 0.21 A for the main body

131 structures are very similar, with an RMSD in backbone atom positions of 1.4 A when loop regions are o

132 ced are very well converged with the RMSD of backbone atom positions of the main body of the peptide

133 more, the relatively small changes in Calpha backbone atom positions which were observed in these mut

134 mber of backbone atoms and the identities of backbone atoms relative to a poly-alpha-amino acid backb

135 .7-1.8 A root mean square deviations for the backbone atoms relative to the experimentally determined

136 The global root-mean-square deviation of the backbone atoms relative to the X-ray structure is 1.4 A.

137 a few notable and significant exceptions for backbone atoms residing within the proteins' DNA-binding

138 Backbone-atom resonances have been assigned for both the

139 modules are well-ordered structures, having backbone atom rmsd values from the mean structure of 0.5

140 anner agrees with the X-ray structure with a backbone atom root-mean-square deviation of 1.8 A.

141 ifs to encase and wrench open the RNA, while backbone atoms specify the uridine bases.

142 en though the model computations omitted the backbone atoms (suggesting that the backbone in B-form D

143 Common backbone atom superimpositions of structures derived fro

144 phenol hydroxylase system (RMSD = 2.48 A for backbone atoms), that of MMOB reveals a considerably mor

145 At the level of backbone atoms, the liganded closed-channel model presen

146 so decrease the solvent accessibility of the backbone atoms, thereby stabilizing the secondary struct

147 n the Coulombic interactions between charged backbone atoms; these parameters are adjusted to obtain

148 s such as pi-stacking with Ala117 and Thr118 backbone atoms, van der Waals contacts with Gly114 and A

149 effort to enhance interactions with protease backbone atoms, we have incorporated stereochemically de

150 ound to repeatedly interact with the protein backbone atoms, weakening individual interstrand H-bonds

151 attern of anticorrelated motions for protein backbone atoms when the transition state occupies the ac

152 res are remarkably similar, superimposing on backbone atoms with an rmsd of 0.7 A.

153 root mean square deviation of 1.36 A for all backbone atoms with the corresponding part of the crysta

154 rotamers are then refined together with the backbone atoms with the use of a composite physics- and