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  1. calibration_nmr_pdb/2M1K.pdb +0 -0
  2. calibration_nmr_pdb/2MA9.pdb +0 -0
  3. calibration_nmr_pdb/2MXN.pdb +0 -0
  4. calibration_nmr_pdb/2MXX.pdb +0 -0
  5. calibration_nmr_pdb/2N80.pdb +0 -0
  6. calibration_nmr_pdb/2NCN.pdb +0 -0
  7. calibration_nmr_pdb/2O22.pdb +0 -0
  8. calibration_nmr_pdb/2RLI.pdb +0 -0
  9. calibration_nmr_pdb/2RLL.pdb +338 -0
  10. calibration_nmr_pdb/2RMK.pdb +0 -0
  11. calibration_nmr_pdb/2RNY.pdb +0 -0
  12. calibration_nmr_pdb/2RRS.pdb +0 -0
  13. calibration_nmr_pdb/2RS9.pdb +0 -0
  14. calibration_nmr_pdb/2RVQ.pdb +0 -0
  15. calibration_nmr_pdb/4C7Q.pdb +0 -0
  16. calibration_nmr_pdb/5AJ1.pdb +0 -0
  17. calibration_nmr_pdb/5I8N.pdb +0 -0
  18. calibration_nmr_pdb/5JPW.pdb +0 -0
  19. calibration_nmr_pdb/5JS7.pdb +0 -0
  20. calibration_nmr_pdb/5KJ3.pdb +0 -0
  21. calibration_nmr_pdb/5KK9.pdb +0 -0
  22. calibration_nmr_pdb/5T7C.pdb +0 -0
  23. calibration_nmr_pdb/5XF0.pdb +0 -0
  24. calibration_nmr_pdb/5YFG.pdb +0 -0
  25. calibration_nmr_pdb/6FGP.pdb +0 -0
  26. calibration_nmr_pdb/6HPI.pdb +0 -0
  27. calibration_nmr_pdb/6HQ1.pdb +0 -0
  28. calibration_nmr_pdb/6IB6.pdb +0 -0
  29. calibration_nmr_pdb/6JHD.pdb +0 -0
  30. calibration_nmr_pdb/6K2K.pdb +0 -0
  31. calibration_nmr_pdb/6L8R.pdb +0 -0
  32. calibration_nmr_pdb/6MPP.pdb +0 -0
  33. calibration_nmr_pdb/6N13.pdb +0 -0
  34. calibration_nmr_pdb/6RPV.pdb +0 -0
  35. calibration_nmr_pdb/6ZZE.pdb +0 -0
  36. calibration_nmr_pdb/7DFE.pdb +0 -0
  37. calibration_nmr_pdb/7RNO.pdb +0 -0
  38. calibration_nmr_pdb/8CA0.pdb +0 -0
  39. calibration_nmr_pdb/8K6Z.pdb +0 -0
  40. calibration_nmr_pdb/8U27.pdb +0 -0
  41. confidence_conformation_v5/frozen_manifest_v5_1.json +11 -0
  42. confidence_conformation_v5/rmsf_calibration.json +0 -0
  43. confidence_conformation_v5/rmsf_calibration.md +135 -0
  44. confidence_conformation_v5/rmsf_calibration_1289.json +0 -0
  45. confidence_conformation_v5/rmsf_calibration_1289.md +135 -0
  46. confidence_conformation_v5/rmsf_calibration_entities.json +612 -0
  47. confidence_conformation_v5_clustered/split_audit.json +66 -0
  48. confidence_conformation_v5_clustered/split_manifest.json +1423 -0
  49. confidence_idp_unified/lock.mdb +0 -0
  50. confidence_idp_v3/idp_summary.json +10 -0
calibration_nmr_pdb/2M1K.pdb ADDED
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calibration_nmr_pdb/2MA9.pdb ADDED
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calibration_nmr_pdb/2MXN.pdb ADDED
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calibration_nmr_pdb/2MXX.pdb ADDED
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calibration_nmr_pdb/2N80.pdb ADDED
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calibration_nmr_pdb/2NCN.pdb ADDED
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calibration_nmr_pdb/2O22.pdb ADDED
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calibration_nmr_pdb/2RLI.pdb ADDED
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calibration_nmr_pdb/2RLL.pdb ADDED
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1
+ HEADER MEMBRANE PROTEIN 21-JUL-07 2RLL
2
+ TITLE CCR5 NT(7-15)
3
+ COMPND MOL_ID: 1;
4
+ COMPND 2 MOLECULE: 9-MER FROM C-C CHEMOKINE RECEPTOR TYPE 5;
5
+ COMPND 3 CHAIN: A;
6
+ COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, UNP RESIDUES 7-15;
7
+ COMPND 5 SYNONYM: C-C CKR-5, CC-CKR-5, CCR-5, CCR5, HIV-1 FUSION CORECEPTOR,
8
+ COMPND 6 CHEMR13, CD195 ANTIGEN;
9
+ COMPND 7 ENGINEERED: YES
10
+ SOURCE MOL_ID: 1;
11
+ SOURCE 2 SYNTHETIC: YES;
12
+ SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED BY SOLID
13
+ SOURCE 4 PHASE SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC.; THIS SEQUENCE
14
+ SOURCE 5 OCCURS NATURALLY IN HUMANS.
15
+ KEYWDS HIV-1 CORECEPTOR CCR5 N-TERMINUS BOUND TO GP120:CD4, G-PROTEIN
16
+ KEYWDS 2 COUPLED RECEPTOR, GLYCOPROTEIN, HOST-VIRUS INTERACTION, MEMBRANE,
17
+ KEYWDS 3 POLYMORPHISM, SULFATION, TRANSDUCER, TRANSMEMBRANE, MEMBRANE PROTEIN
18
+ EXPDTA SOLUTION NMR
19
+ MDLTYP MINIMIZED AVERAGE
20
+ AUTHOR C.A.BEWLEY,S.N.LAM
21
+ REVDAT 6 30-OCT-24 2RLL 1 REMARK
22
+ REVDAT 5 15-NOV-23 2RLL 1 ATOM
23
+ REVDAT 4 16-MAR-22 2RLL 1 REMARK LINK
24
+ REVDAT 3 24-FEB-09 2RLL 1 VERSN
25
+ REVDAT 2 16-OCT-07 2RLL 1 JRNL
26
+ REVDAT 1 25-SEP-07 2RLL 0
27
+ JRNL AUTH C.-C.HUANG,S.N.LAM,P.ACHARYA,M.TANG,S.-H.XIANG,S.S.HUSSAN,
28
+ JRNL AUTH 2 R.L.STANFIELD,J.ROBINSON,J.SODROSKI,I.A.WILSON,R.WYATT,
29
+ JRNL AUTH 3 C.A.BEWLEY,P.D.KWONG
30
+ JRNL TITL STRUCTURES OF THE CCR5 N TERMINUS AND OF A TYROSINE-SULFATED
31
+ JRNL TITL 2 ANTIBODY WITH HIV-1 GP120 AND CD4
32
+ JRNL REF SCIENCE V. 317 1930 2007
33
+ JRNL REFN ISSN 0036-8075
34
+ JRNL PMID 17901336
35
+ JRNL DOI 10.1126/SCIENCE.1145373
36
+ REMARK 2
37
+ REMARK 2 RESOLUTION. NOT APPLICABLE.
38
+ REMARK 3
39
+ REMARK 3 REFINEMENT.
40
+ REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH
41
+ REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR
42
+ REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-
43
+ REMARK 3 PLOR NIH)
44
+ REMARK 3
45
+ REMARK 3 OTHER REFINEMENT REMARKS: NULL
46
+ REMARK 4
47
+ REMARK 4 2RLL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
48
+ REMARK 100
49
+ REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-07.
50
+ REMARK 100 THE DEPOSITION ID IS D_1000150007.
51
+ REMARK 210
52
+ REMARK 210 EXPERIMENTAL DETAILS
53
+ REMARK 210 EXPERIMENT TYPE : NMR
54
+ REMARK 210 TEMPERATURE (KELVIN) : 300
55
+ REMARK 210 PH : 6.8
56
+ REMARK 210 IONIC STRENGTH : 50MM NACL
57
+ REMARK 210 PRESSURE : AMBIENT
58
+ REMARK 210 SAMPLE CONTENTS : 800UM PROTEIN; 90% H2O, 10% D2O
59
+ REMARK 210
60
+ REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-1H TOCSY;
61
+ REMARK 210 2D 1H-1H NOESY; 2D 1H-1H COSY
62
+ REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
63
+ REMARK 210 SPECTROMETER MODEL : AVANCE
64
+ REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
65
+ REMARK 210
66
+ REMARK 210 STRUCTURE DETERMINATION.
67
+ REMARK 210 SOFTWARE USED : NULL
68
+ REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
69
+ REMARK 210
70
+ REMARK 210 CONFORMERS, NUMBER CALCULATED : 30
71
+ REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
72
+ REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
73
+ REMARK 210 RESTRAINT VIOLATIONS
74
+ REMARK 210
75
+ REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
76
+ REMARK 210
77
+ REMARK 210 REMARK: NULL
78
+ REMARK 215
79
+ REMARK 215 NMR STUDY
80
+ REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
81
+ REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
82
+ REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
83
+ REMARK 215 THESE RECORDS ARE MEANINGLESS.
84
+ REMARK 300
85
+ REMARK 300 BIOMOLECULE: 1
86
+ REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
87
+ REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
88
+ REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
89
+ REMARK 300 BURIED SURFACE AREA.
90
+ REMARK 350
91
+ REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
92
+ REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
93
+ REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
94
+ REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
95
+ REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
96
+ REMARK 350
97
+ REMARK 350 BIOMOLECULE: 1
98
+ REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
99
+ REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
100
+ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
101
+ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
102
+ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
103
+ DBREF 2RLL A 7 15 UNP P51681 CCR5_HUMAN 7 15
104
+ SEQRES 1 A 9 SER PRO ILE TYS ASP ILE ASN TYS TYR
105
+ MODRES 2RLL TYS A 10 TYR O-SULFO-L-TYROSINE
106
+ MODRES 2RLL TYS A 14 TYR O-SULFO-L-TYROSINE
107
+ HET TYS A 10 24
108
+ HET TYS A 14 24
109
+ HETNAM TYS O-SULFO-L-TYROSINE
110
+ FORMUL 1 TYS 2(C9 H11 N O6 S)
111
+ HELIX 1 1 PRO A 8 TYR A 15 1 8
112
+ LINK C ILE A 9 N TYS A 10 1555 1555 1.31
113
+ LINK C TYS A 10 N ASP A 11 1555 1555 1.31
114
+ LINK C ASN A 13 N TYS A 14 1555 1555 1.31
115
+ LINK C TYS A 14 N TYR A 15 1555 1555 1.31
116
+ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
117
+ ORIGX1 1.000000 0.000000 0.000000 0.00000
118
+ ORIGX2 0.000000 1.000000 0.000000 0.00000
119
+ ORIGX3 0.000000 0.000000 1.000000 0.00000
120
+ SCALE1 1.000000 0.000000 0.000000 0.00000
121
+ SCALE2 0.000000 1.000000 0.000000 0.00000
122
+ SCALE3 0.000000 0.000000 1.000000 0.00000
123
+ ATOM 1 N SER A 7 -2.730 -6.604 -12.853 1.00 3.79 N
124
+ ATOM 2 CA SER A 7 -1.255 -6.792 -12.947 1.00 3.23 C
125
+ ATOM 3 C SER A 7 -0.751 -6.315 -14.319 1.00 2.13 C
126
+ ATOM 4 O SER A 7 0.313 -5.737 -14.421 1.00 2.40 O
127
+ ATOM 5 CB SER A 7 -0.915 -8.279 -12.745 1.00 3.73 C
128
+ ATOM 6 OG SER A 7 -2.114 -9.042 -12.773 1.00 4.16 O
129
+ ATOM 7 H1 SER A 7 -3.020 -5.820 -13.471 1.00 4.23 H
130
+ ATOM 8 H2 SER A 7 -2.989 -6.385 -11.869 1.00 3.98 H
131
+ ATOM 9 H3 SER A 7 -3.211 -7.475 -13.153 1.00 4.07 H
132
+ ATOM 10 HA SER A 7 -0.777 -6.208 -12.174 1.00 3.72 H
133
+ ATOM 11 HB2 SER A 7 -0.261 -8.621 -13.531 1.00 3.86 H
134
+ ATOM 12 HB3 SER A 7 -0.420 -8.408 -11.791 1.00 4.17 H
135
+ ATOM 13 HG SER A 7 -2.770 -8.583 -12.241 1.00 4.37 H
136
+ ATOM 14 N PRO A 8 -1.498 -6.560 -15.368 1.00 1.47 N
137
+ ATOM 15 CA PRO A 8 -1.106 -6.154 -16.741 1.00 1.06 C
138
+ ATOM 16 C PRO A 8 -1.552 -4.728 -17.082 1.00 0.74 C
139
+ ATOM 17 O PRO A 8 -2.657 -4.504 -17.537 1.00 0.71 O
140
+ ATOM 18 CB PRO A 8 -1.828 -7.173 -17.622 1.00 2.07 C
141
+ ATOM 19 CG PRO A 8 -3.044 -7.592 -16.848 1.00 2.54 C
142
+ ATOM 20 CD PRO A 8 -2.797 -7.248 -15.369 1.00 2.27 C
143
+ ATOM 21 HA PRO A 8 -0.042 -6.256 -16.873 1.00 1.46 H
144
+ ATOM 22 HB2 PRO A 8 -2.116 -6.716 -18.561 1.00 2.53 H
145
+ ATOM 23 HB3 PRO A 8 -1.193 -8.026 -17.801 1.00 2.55 H
146
+ ATOM 24 HG2 PRO A 8 -3.913 -7.058 -17.211 1.00 3.25 H
147
+ ATOM 25 HG3 PRO A 8 -3.199 -8.655 -16.950 1.00 2.92 H
148
+ ATOM 26 HD2 PRO A 8 -3.577 -6.593 -15.005 1.00 3.00 H
149
+ ATOM 27 HD3 PRO A 8 -2.745 -8.146 -14.774 1.00 2.42 H
150
+ ATOM 28 N ILE A 9 -0.698 -3.765 -16.868 1.00 0.68 N
151
+ ATOM 29 CA ILE A 9 -1.065 -2.355 -17.182 1.00 0.65 C
152
+ ATOM 30 C ILE A 9 -1.337 -2.222 -18.682 1.00 0.43 C
153
+ ATOM 31 O ILE A 9 -2.109 -1.388 -19.112 1.00 0.53 O
154
+ ATOM 32 CB ILE A 9 0.085 -1.427 -16.787 1.00 0.90 C
155
+ ATOM 33 CG1 ILE A 9 0.335 -1.543 -15.280 1.00 1.16 C
156
+ ATOM 34 CG2 ILE A 9 -0.285 0.016 -17.133 1.00 1.12 C
157
+ ATOM 35 CD1 ILE A 9 1.602 -0.769 -14.907 1.00 1.43 C
158
+ ATOM 36 H ILE A 9 0.188 -3.969 -16.504 1.00 0.83 H
159
+ ATOM 37 HA ILE A 9 -1.953 -2.083 -16.630 1.00 0.81 H
160
+ ATOM 38 HB ILE A 9 0.977 -1.710 -17.326 1.00 0.90 H
161
+ ATOM 39 HG12 ILE A 9 -0.508 -1.133 -14.743 1.00 1.30 H
162
+ ATOM 40 HG13 ILE A 9 0.459 -2.582 -15.015 1.00 1.12 H
163
+ ATOM 41 HG21 ILE A 9 0.316 0.694 -16.545 1.00 1.50 H
164
+ ATOM 42 HG22 ILE A 9 -1.329 0.182 -16.917 1.00 1.56 H
165
+ ATOM 43 HG23 ILE A 9 -0.101 0.193 -18.183 1.00 1.59 H
166
+ ATOM 44 HD11 ILE A 9 1.565 -0.501 -13.862 1.00 1.84 H
167
+ ATOM 45 HD12 ILE A 9 1.667 0.127 -15.506 1.00 1.84 H
168
+ ATOM 46 HD13 ILE A 9 2.468 -1.388 -15.089 1.00 1.76 H
169
+ HETATM 47 N TYS A 10 -0.706 -3.037 -19.482 1.00 0.31 N
170
+ HETATM 48 CA TYS A 10 -0.923 -2.958 -20.955 1.00 0.43 C
171
+ HETATM 49 CB TYS A 10 0.002 -3.959 -21.659 1.00 0.65 C
172
+ HETATM 50 CG TYS A 10 1.333 -3.308 -21.961 1.00 0.88 C
173
+ HETATM 51 CD1 TYS A 10 1.882 -2.383 -21.065 1.00 1.66 C
174
+ HETATM 52 CD2 TYS A 10 2.018 -3.635 -23.137 1.00 1.47 C
175
+ HETATM 53 CE1 TYS A 10 3.117 -1.785 -21.346 1.00 1.89 C
176
+ HETATM 54 CE2 TYS A 10 3.252 -3.037 -23.419 1.00 1.62 C
177
+ HETATM 55 CZ TYS A 10 3.802 -2.112 -22.523 1.00 1.43 C
178
+ HETATM 56 OH TYS A 10 5.020 -1.524 -22.799 1.00 1.72 O
179
+ HETATM 57 S TYS A 10 4.774 -0.452 -24.273 1.00 2.22 S
180
+ HETATM 58 O1 TYS A 10 4.072 -1.228 -25.303 1.00 2.94 O
181
+ HETATM 59 O2 TYS A 10 6.080 -0.006 -24.790 1.00 2.57 O
182
+ HETATM 60 O3 TYS A 10 3.971 0.726 -23.904 1.00 2.79 O
183
+ HETATM 61 C TYS A 10 -2.382 -3.304 -21.271 1.00 0.35 C
184
+ HETATM 62 O TYS A 10 -2.950 -2.824 -22.232 1.00 0.46 O
185
+ HETATM 63 H2 TYS A 10 -0.086 -3.701 -19.114 1.00 0.37 H
186
+ HETATM 64 HA TYS A 10 -0.706 -1.958 -21.300 1.00 0.60 H
187
+ HETATM 65 HB2 TYS A 10 0.159 -4.813 -21.018 1.00 0.64 H
188
+ HETATM 66 HB3 TYS A 10 -0.453 -4.284 -22.583 1.00 0.80 H
189
+ HETATM 67 HD1 TYS A 10 1.354 -2.130 -20.158 1.00 2.40 H
190
+ HETATM 68 HD2 TYS A 10 1.594 -4.349 -23.828 1.00 2.23 H
191
+ HETATM 69 HE1 TYS A 10 3.541 -1.072 -20.655 1.00 2.73 H
192
+ HETATM 70 HE2 TYS A 10 3.779 -3.290 -24.326 1.00 2.35 H
193
+ ATOM 71 N ASP A 11 -2.990 -4.135 -20.470 1.00 0.31 N
194
+ ATOM 72 CA ASP A 11 -4.410 -4.513 -20.724 1.00 0.35 C
195
+ ATOM 73 C ASP A 11 -5.267 -3.250 -20.823 1.00 0.32 C
196
+ ATOM 74 O ASP A 11 -6.208 -3.186 -21.589 1.00 0.31 O
197
+ ATOM 75 CB ASP A 11 -4.919 -5.384 -19.573 1.00 0.41 C
198
+ ATOM 76 CG ASP A 11 -6.292 -5.955 -19.933 1.00 0.59 C
199
+ ATOM 77 OD1 ASP A 11 -6.721 -5.749 -21.056 1.00 1.29 O
200
+ ATOM 78 OD2 ASP A 11 -6.890 -6.589 -19.079 1.00 1.20 O
201
+ ATOM 79 H ASP A 11 -2.513 -4.512 -19.701 1.00 0.37 H
202
+ ATOM 80 HA ASP A 11 -4.475 -5.065 -21.649 1.00 0.44 H
203
+ ATOM 81 HB2 ASP A 11 -4.224 -6.194 -19.401 1.00 0.44 H
204
+ ATOM 82 HB3 ASP A 11 -5.003 -4.786 -18.679 1.00 0.41 H
205
+ ATOM 83 N ILE A 12 -4.955 -2.245 -20.051 1.00 0.36 N
206
+ ATOM 84 CA ILE A 12 -5.758 -0.991 -20.101 1.00 0.37 C
207
+ ATOM 85 C ILE A 12 -5.813 -0.470 -21.539 1.00 0.30 C
208
+ ATOM 86 O ILE A 12 -6.844 -0.032 -22.010 1.00 0.29 O
209
+ ATOM 87 CB ILE A 12 -5.112 0.066 -19.203 1.00 0.49 C
210
+ ATOM 88 CG1 ILE A 12 -5.094 -0.436 -17.757 1.00 0.62 C
211
+ ATOM 89 CG2 ILE A 12 -5.917 1.364 -19.283 1.00 0.50 C
212
+ ATOM 90 CD1 ILE A 12 -4.303 0.541 -16.886 1.00 0.75 C
213
+ ATOM 91 H ILE A 12 -4.195 -2.316 -19.437 1.00 0.43 H
214
+ ATOM 92 HA ILE A 12 -6.761 -1.192 -19.753 1.00 0.36 H
215
+ ATOM 93 HB ILE A 12 -4.100 0.250 -19.536 1.00 0.54 H
216
+ ATOM 94 HG12 ILE A 12 -6.107 -0.509 -17.390 1.00 0.63 H
217
+ ATOM 95 HG13 ILE A 12 -4.626 -1.409 -17.719 1.00 0.64 H
218
+ ATOM 96 HG21 ILE A 12 -5.729 1.847 -20.231 1.00 1.09 H
219
+ ATOM 97 HG22 ILE A 12 -5.621 2.022 -18.480 1.00 1.19 H
220
+ ATOM 98 HG23 ILE A 12 -6.970 1.140 -19.196 1.00 1.14 H
221
+ ATOM 99 HD11 ILE A 12 -3.444 0.899 -17.434 1.00 1.15 H
222
+ ATOM 100 HD12 ILE A 12 -3.974 0.038 -15.988 1.00 1.36 H
223
+ ATOM 101 HD13 ILE A 12 -4.933 1.377 -16.619 1.00 1.30 H
224
+ ATOM 102 N ASN A 13 -4.714 -0.510 -22.242 1.00 0.40 N
225
+ ATOM 103 CA ASN A 13 -4.715 -0.012 -23.647 1.00 0.42 C
226
+ ATOM 104 C ASN A 13 -5.776 -0.764 -24.453 1.00 0.31 C
227
+ ATOM 105 O ASN A 13 -6.492 -0.186 -25.246 1.00 0.36 O
228
+ ATOM 106 CB ASN A 13 -3.338 -0.247 -24.272 1.00 0.65 C
229
+ ATOM 107 CG ASN A 13 -3.240 0.520 -25.593 1.00 0.78 C
230
+ ATOM 108 OD1 ASN A 13 -4.117 1.291 -25.927 1.00 1.26 O
231
+ ATOM 109 ND2 ASN A 13 -2.202 0.339 -26.362 1.00 1.23 N
232
+ ATOM 110 H ASN A 13 -3.890 -0.864 -21.846 1.00 0.51 H
233
+ ATOM 111 HA ASN A 13 -4.939 1.044 -23.654 1.00 0.47 H
234
+ ATOM 112 HB2 ASN A 13 -2.571 0.101 -23.595 1.00 0.80 H
235
+ ATOM 113 HB3 ASN A 13 -3.203 -1.301 -24.460 1.00 0.67 H
236
+ ATOM 114 HD21 ASN A 13 -1.495 -0.283 -26.093 1.00 1.79 H
237
+ ATOM 115 HD22 ASN A 13 -2.130 0.826 -27.210 1.00 1.32 H
238
+ HETATM 116 N TYS A 14 -5.886 -2.049 -24.254 1.00 0.40 N
239
+ HETATM 117 CA TYS A 14 -6.904 -2.835 -25.006 1.00 0.54 C
240
+ HETATM 118 CB TYS A 14 -6.782 -4.315 -24.641 1.00 0.78 C
241
+ HETATM 119 CG TYS A 14 -7.747 -5.120 -25.479 1.00 0.95 C
242
+ HETATM 120 CD1 TYS A 14 -9.018 -5.428 -24.982 1.00 1.62 C
243
+ HETATM 121 CD2 TYS A 14 -7.369 -5.556 -26.755 1.00 1.65 C
244
+ HETATM 122 CE1 TYS A 14 -9.913 -6.173 -25.760 1.00 1.89 C
245
+ HETATM 123 CE2 TYS A 14 -8.263 -6.302 -27.533 1.00 1.97 C
246
+ HETATM 124 CZ TYS A 14 -9.535 -6.610 -27.035 1.00 1.72 C
247
+ HETATM 125 OH TYS A 14 -10.416 -7.344 -27.802 1.00 2.18 O
248
+ HETATM 126 S TYS A 14 -10.678 -8.941 -26.930 1.00 2.85 S
249
+ HETATM 127 O1 TYS A 14 -9.521 -9.194 -26.062 1.00 3.45 O
250
+ HETATM 128 O2 TYS A 14 -10.811 -10.031 -27.912 1.00 3.24 O
251
+ HETATM 129 O3 TYS A 14 -11.904 -8.869 -26.114 1.00 3.44 O
252
+ HETATM 130 C TYS A 14 -8.303 -2.333 -24.643 1.00 0.53 C
253
+ HETATM 131 O TYS A 14 -9.170 -2.214 -25.486 1.00 0.65 O
254
+ HETATM 132 H2 TYS A 14 -5.301 -2.497 -23.608 1.00 0.49 H
255
+ HETATM 133 HA TYS A 14 -6.742 -2.711 -26.067 1.00 0.63 H
256
+ HETATM 134 HB2 TYS A 14 -5.773 -4.651 -24.829 1.00 0.95 H
257
+ HETATM 135 HB3 TYS A 14 -7.017 -4.449 -23.595 1.00 0.99 H
258
+ HETATM 136 HD1 TYS A 14 -9.310 -5.091 -23.998 1.00 2.34 H
259
+ HETATM 137 HD2 TYS A 14 -6.388 -5.319 -27.138 1.00 2.35 H
260
+ HETATM 138 HE1 TYS A 14 -10.894 -6.411 -25.376 1.00 2.65 H
261
+ HETATM 139 HE2 TYS A 14 -7.972 -6.639 -28.517 1.00 2.77 H
262
+ ATOM 140 N TYR A 15 -8.530 -2.041 -23.391 1.00 0.58 N
263
+ ATOM 141 CA TYR A 15 -9.872 -1.551 -22.969 1.00 0.81 C
264
+ ATOM 142 C TYR A 15 -10.291 -0.380 -23.860 1.00 0.93 C
265
+ ATOM 143 O TYR A 15 -9.471 0.497 -24.077 1.00 1.62 O
266
+ ATOM 144 CB TYR A 15 -9.807 -1.087 -21.512 1.00 0.99 C
267
+ ATOM 145 CG TYR A 15 -11.197 -0.753 -21.026 1.00 0.91 C
268
+ ATOM 146 CD1 TYR A 15 -12.019 -1.761 -20.509 1.00 1.51 C
269
+ ATOM 147 CD2 TYR A 15 -11.664 0.566 -21.092 1.00 1.21 C
270
+ ATOM 148 CE1 TYR A 15 -13.307 -1.451 -20.057 1.00 2.00 C
271
+ ATOM 149 CE2 TYR A 15 -12.952 0.875 -20.640 1.00 1.72 C
272
+ ATOM 150 CZ TYR A 15 -13.774 -0.133 -20.123 1.00 2.01 C
273
+ ATOM 151 OH TYR A 15 -15.043 0.172 -19.678 1.00 2.70 O
274
+ ATOM 152 OXT TYR A 15 -11.426 -0.379 -24.308 1.00 1.31 O
275
+ ATOM 153 H TYR A 15 -7.816 -2.147 -22.728 1.00 0.55 H
276
+ ATOM 154 HA TYR A 15 -10.593 -2.350 -23.061 1.00 1.00 H
277
+ ATOM 155 HB2 TYR A 15 -9.393 -1.876 -20.901 1.00 1.45 H
278
+ ATOM 156 HB3 TYR A 15 -9.182 -0.210 -21.441 1.00 1.30 H
279
+ ATOM 157 HD1 TYR A 15 -11.658 -2.778 -20.458 1.00 1.90 H
280
+ ATOM 158 HD2 TYR A 15 -11.030 1.344 -21.491 1.00 1.52 H
281
+ ATOM 159 HE1 TYR A 15 -13.941 -2.229 -19.658 1.00 2.60 H
282
+ ATOM 160 HE2 TYR A 15 -13.312 1.892 -20.691 1.00 2.19 H
283
+ ATOM 161 HH TYR A 15 -15.606 0.293 -20.446 1.00 2.99 H
284
+ TER 162 TYR A 15
285
+ CONECT 30 47
286
+ CONECT 47 30 48 63
287
+ CONECT 48 47 49 61 64
288
+ CONECT 49 48 50 65 66
289
+ CONECT 50 49 51 52
290
+ CONECT 51 50 53 67
291
+ CONECT 52 50 54 68
292
+ CONECT 53 51 55 69
293
+ CONECT 54 52 55 70
294
+ CONECT 55 53 54 56
295
+ CONECT 56 55 57
296
+ CONECT 57 56 58 59 60
297
+ CONECT 58 57
298
+ CONECT 59 57
299
+ CONECT 60 57
300
+ CONECT 61 48 62 71
301
+ CONECT 62 61
302
+ CONECT 63 47
303
+ CONECT 64 48
304
+ CONECT 65 49
305
+ CONECT 66 49
306
+ CONECT 67 51
307
+ CONECT 68 52
308
+ CONECT 69 53
309
+ CONECT 70 54
310
+ CONECT 71 61
311
+ CONECT 104 116
312
+ CONECT 116 104 117 132
313
+ CONECT 117 116 118 130 133
314
+ CONECT 118 117 119 134 135
315
+ CONECT 119 118 120 121
316
+ CONECT 120 119 122 136
317
+ CONECT 121 119 123 137
318
+ CONECT 122 120 124 138
319
+ CONECT 123 121 124 139
320
+ CONECT 124 122 123 125
321
+ CONECT 125 124 126
322
+ CONECT 126 125 127 128 129
323
+ CONECT 127 126
324
+ CONECT 128 126
325
+ CONECT 129 126
326
+ CONECT 130 117 131 140
327
+ CONECT 131 130
328
+ CONECT 132 116
329
+ CONECT 133 117
330
+ CONECT 134 118
331
+ CONECT 135 118
332
+ CONECT 136 120
333
+ CONECT 137 121
334
+ CONECT 138 122
335
+ CONECT 139 123
336
+ CONECT 140 130
337
+ MASTER 67 0 2 1 0 0 0 6 90 1 52 1
338
+ END
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confidence_conformation_v5/frozen_manifest_v5_1.json ADDED
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "version": "v5.1",
3
+ "status": "frozen",
4
+ "count": 1289,
5
+ "unique_pdb_ids": 1289,
6
+ "unique_sequences": 1289,
7
+ "canonical_fingerprint_algorithm": "sha256 of LMDB-index-ordered pdb_id\\tsequence records joined by newline",
8
+ "canonical_fingerprint": "1184e7a3c5edfacc2f0f6266421ca0c0864f021b0b2878495f23e75cecc4336c",
9
+ "previously_recorded_fingerprint": "ece2c993d695ef1989dba0c11f5eb8bb97eafb9d168ef9a8d180a06d5bbf61b6",
10
+ "build_stopped_at_count": 1289
11
+ }
confidence_conformation_v5/rmsf_calibration.json ADDED
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confidence_conformation_v5/rmsf_calibration.md ADDED
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1
+ # AF2-RMSF Experimental Ensemble Calibration
2
+
3
+ - Verdict: `rank_only`
4
+ - Calibrated proteins: 121
5
+ - Median Spearman: 0.21704889295022123
6
+ - Median partial Spearman controlling 1-pLDDT: 0.14851839694428695
7
+ - Median top-20% recall: 0.3076923076923077
8
+ - Median flexible-region AUROC: 0.627951256664128
9
+ - Annotated-IDP subset: {'n_proteins': 19, 'median_spearman': 0.16504242848394715, 'median_top20_recall': 0.26666666666666666, 'median_flexible_auc': 0.5802103879026956, 'median_uncertainty_spearman': -0.060834692788680665, 'median_partial_spearman': 0.21536240205703797, 'median_spearman_ci95': [-0.17145721925133692, 0.41574232894987606], 'median_top20_recall_ci95': [0.1724137931034483, 0.4117647058823529], 'median_flexible_auc_ci95': [0.4690265486725664, 0.7205882352941176], 'median_partial_spearman_ci95': [0.001501885448866303, 0.248346590118742], 'verdict': 'rank_only'}
10
+ - Important limitation: deposited NMR models are restraint-compatible ensembles, not Boltzmann-weighted trajectories.
11
+ - MSA-depth confounding is not measured because the source LMDB does not retain MSA depth.
12
+
13
+ | UniProt | PDB | Models | Residues | Spearman | Partial | Top20 | AUROC |
14
+ |---|---:|---:|---:|---:|---:|---:|---:|
15
+ | A1B602 | 2LL0 | 20 | 104 | -0.3571001813720261 | 0.12300224047796865 | 0.000 | 0.194 |
16
+ | A5Y0M2 | 7DFE | 10 | 142 | 0.14132915331596785 | 0.21536240205703797 | 0.172 | 0.469 |
17
+ | A8AZZ3 | 2MXX | 20 | 171 | 0.5731994144046849 | 0.5311709506323951 | 0.571 | 0.870 |
18
+ | C9ZXG5 | 2MXN | 20 | 142 | 0.5305737115746106 | 0.45626384403729325 | 0.724 | 0.845 |
19
+ | D6PZY5 | 4C7Q | 20 | 85 | 0.42071526284932576 | 0.2395348837209302 | 0.412 | 0.721 |
20
+ | E9AD06 | 2M5R | 20 | 78 | 0.2828184473754094 | 0.248346590118742 | 0.188 | 0.649 |
21
+ | G1K3N3 | 2LC2 | 20 | 108 | 0.6861966141739785 | 0.41577829222517554 | 0.409 | 0.847 |
22
+ | G8HXD9 | 2LFW | 15 | 56 | 0.6019822282980178 | 0.23451811346548188 | 0.667 | 0.790 |
23
+ | O00244 | 1TL4 | 30 | 68 | 0.378134900942856 | 0.07939840439745009 | 0.571 | 0.734 |
24
+ | O14618 | 2CRL | 20 | 86 | 0.6742110476909289 | 0.12599650926930517 | 0.500 | 0.819 |
25
+ | O14893 | 2LEH | 32 | 186 | 0.6115157420660267 | 0.44113684151634813 | 0.342 | 0.773 |
26
+ | O14907 | 2KG2 | 20 | 123 | 0.38928299647882786 | 0.3135584475887065 | 0.440 | 0.722 |
27
+ | O14933 | 2KJH | 16 | 150 | 0.19202453442375217 | 0.22561536068269702 | 0.233 | 0.564 |
28
+ | O43819 | 2RLI | 31 | 167 | 0.4262086841806921 | 0.1402779638657281 | 0.412 | 0.699 |
29
+ | O75365 | 1R6H | 20 | 169 | 0.5448063248968228 | 0.3865695390582269 | 0.471 | 0.685 |
30
+ | O75771 | 2KZ3 | 20 | 83 | 0.09487427060157004 | 0.18116367910667058 | 0.118 | 0.577 |
31
+ | O95166 | 1KLV | 20 | 100 | 0.45202520252025197 | 0.2655385538553855 | 0.500 | 0.604 |
32
+ | O95881 | 2K8V | 40 | 149 | 0.5084745147832396 | 0.35463450027208415 | 0.400 | 0.695 |
33
+ | P00374 | 1YHO | 25 | 186 | 0.20875196397018028 | 0.303386187636662 | 0.395 | 0.684 |
34
+ | P00441 | 1BA9 | 36 | 148 | 0.19369060883921865 | 0.06050633567412091 | 0.167 | 0.596 |
35
+ | P01034 | 6RPV | 20 | 119 | 0.11714143284432418 | 0.1290129611166501 | 0.167 | 0.468 |
36
+ | P01215 | 1DZ7 | 27 | 92 | -0.03722084367245657 | -0.004700769076645654 | 0.105 | 0.373 |
37
+ | P02649 | 1OEF | 5 | 24 | 0.12347826086956522 | 0.04347826086956521 | 0.600 | 0.653 |
38
+ | P03950 | 1AWZ | 30 | 123 | 0.31921424978395735 | 0.23658278624034257 | 0.480 | 0.767 |
39
+ | P04083 | 1BO9 | 21 | 73 | 0.32006664198445023 | 0.3088670862643466 | 0.467 | 0.756 |
40
+ | P04439 | 6MPP | 10 | 259 | 0.14270750451518296 | 0.017338261698104273 | 0.288 | 0.633 |
41
+ | P04637 | 1DT7 | 40 | 22 | -0.4116318464144552 | -0.28514963297572 | 0.200 | 0.259 |
42
+ | P05112 | 1BCN | 22 | 127 | 0.22355994563179601 | -0.19875445256842894 | 0.308 | 0.641 |
43
+ | P05231 | 2IL6 | 32 | 166 | -0.17383895953984696 | -0.08241436076368623 | 0.118 | 0.249 |
44
+ | P05412 | 1JUN | 7 | 39 | -0.7163967611336033 | -0.6384615384615385 | 0.000 | 0.113 |
45
+ | P05452 | 1RJH | 20 | 117 | 0.2560505926958294 | 0.4104437351076743 | 0.375 | 0.573 |
46
+ | P06702 | 5I8N | 10 | 113 | 0.5331109854281723 | -0.03429203539823009 | 0.739 | 0.936 |
47
+ | P06703 | 2M1K | 20 | 88 | 0.6698601669543166 | 0.5188968335035752 | 0.500 | 0.842 |
48
+ | P06730 | 2GPQ | 10 | 217 | 0.22516875942445638 | -0.07167049516857152 | 0.295 | 0.603 |
49
+ | P06748 | 2LLH | 20 | 70 | 0.16504242848394715 | 0.5857930189834659 | 0.286 | 0.495 |
50
+ | P06899 | 2RVQ | 10 | 126 | 0.4280374953130859 | 0.4586936632920885 | 0.423 | 0.786 |
51
+ | P07305 | 6HQ1 | 20 | 74 | 0.27460940392447236 | 0.23465383191410583 | 0.267 | 0.641 |
52
+ | P07737 | 1PFL | 20 | 139 | 0.14278117878368113 | 0.07430180079538852 | 0.179 | 0.456 |
53
+ | P07910 | 1TXP | 20 | 27 | -0.4975579975579975 | -0.4554334554334554 | 0.000 | 0.143 |
54
+ | P07998 | 2K11 | 20 | 127 | 0.24889271653543305 | 0.22090012185976754 | 0.577 | 0.732 |
55
+ | P08034 | 5KK9 | 20 | 21 | -0.5194805194805194 | -0.6090909090909091 | 0.200 | 0.287 |
56
+ | P09651 | 2LYV | 20 | 195 | -0.011207496479955979 | 0.001501885448866303 | 0.154 | 0.580 |
57
+ | P09936 | 2LEN | 20 | 222 | 0.07737825279371047 | 0.11693468116575478 | 0.222 | 0.485 |
58
+ | P10415 | 8U27 | 20 | 165 | 0.47792589426441917 | 0.4950418080303476 | 0.424 | 0.728 |
59
+ | P10599 | 1CQG | 35 | 100 | 0.39157515751575156 | 0.23488748874887486 | 0.450 | 0.799 |
60
+ | P14174 | 8CA0 | 4 | 114 | 0.1754966485085357 | 0.12648184524412223 | 0.261 | 0.609 |
61
+ | P15309 | 2L3H | 8 | 39 | -0.018218623481781375 | 0.007085020242914981 | 0.250 | 0.496 |
62
+ | P16220 | 2LXT | 20 | 33 | -0.17145721925133692 | -0.0945855614973262 | 0.429 | 0.434 |
63
+ | P18510 | 1IRP | 12 | 152 | 0.23314128718758326 | 0.10105317832954024 | 0.226 | 0.541 |
64
+ | P20472 | 1RJV | 19 | 110 | 0.11157496111624551 | 0.013105515857809436 | 0.364 | 0.673 |
65
+ | P21730 | 2K3U | 25 | 20 | -0.35939849624060144 | -0.21353383458646616 | 0.250 | 0.391 |
66
+ | P21796 | 2K4T | 20 | 283 | 0.5063703777434927 | 0.4227845836011482 | 0.333 | 0.704 |
67
+ | P23297 | 2L0P | 20 | 93 | 0.21658559875861652 | 0.14851839694428695 | 0.474 | 0.678 |
68
+ | P23396 | 1WH9 | 20 | 79 | -0.1785053554040896 | -0.23264362220058424 | 0.250 | 0.384 |
69
+ | P26447 | 1M31 | 20 | 101 | 0.6716715200931858 | 0.7165637740244611 | 0.667 | 0.898 |
70
+ | P26992 | 1UC6 | 21 | 103 | -0.13791020515749242 | -0.20854017484514342 | 0.000 | 0.440 |
71
+ | P29033 | 5KJ3 | 20 | 22 | -0.13382269904009036 | -0.0378317334839074 | 0.000 | 0.188 |
72
+ | P32881 | 6JHD | 15 | 166 | 0.5898393792917999 | 0.42173396908264527 | 0.500 | 0.819 |
73
+ | P33763 | 2KAX | 31 | 92 | 0.6792380130388546 | 0.4286176656443136 | 0.526 | 0.890 |
74
+ | P35414 | 2LOT | 40 | 55 | 0.5257575757575759 | -0.0546897546897547 | 0.545 | 0.750 |
75
+ | P35613 | 5XF0 | 20 | 107 | -0.1687924920159094 | -0.06864358627716059 | 0.045 | 0.425 |
76
+ | P37235 | 5T7C | 10 | 185 | 0.20576930366551682 | 0.19398051628065655 | 0.324 | 0.571 |
77
+ | P37802 | 1WYM | 20 | 142 | 0.4652413813336798 | 0.31792091636263053 | 0.276 | 0.724 |
78
+ | P37840 | 2KKW | 34 | 140 | -0.3072139249087053 | -0.1366206730664101 | 0.143 | 0.494 |
79
+ | P41159 | 8K6Z | 10 | 146 | -0.20045887036912075 | -0.18965806445393465 | 0.100 | 0.282 |
80
+ | P43897 | 2CP9 | 20 | 52 | 0.4559890719713139 | 0.4657218475198497 | 0.545 | 0.763 |
81
+ | P49795 | 1CMZ | 20 | 128 | 0.07169588903131294 | 0.09658830800219739 | 0.308 | 0.616 |
82
+ | P51681 | 6FGP | 10 | 24 | -0.09391304347826085 | 0.013913043478260868 | 0.200 | 0.474 |
83
+ | P51809 | 2DMW | 20 | 117 | -0.0005245095835393907 | -0.0835618696518755 | 0.458 | 0.560 |
84
+ | P52565 | 2N80 | 10 | 174 | -0.4450821492639312 | -0.32363449984338954 | 0.057 | 0.170 |
85
+ | P55000 | 6ZZE | 20 | 81 | 0.19911924119241192 | 0.15259710930442638 | 0.118 | 0.481 |
86
+ | P56278 | 1QTT | 20 | 107 | 0.5325927232116617 | 0.16265992672270224 | 0.591 | 0.835 |
87
+ | P57730 | 1DGN | 20 | 89 | 0.45240040858018393 | 0.42521280217909435 | 0.556 | 0.776 |
88
+ | P60880 | 2N1T | 5 | 74 | -0.22416882636060712 | -0.28619029988893 | 0.267 | 0.427 |
89
+ | P61769 | 1JNJ | 20 | 99 | 0.15628942486085343 | -0.004650587507730364 | 0.300 | 0.647 |
90
+ | P61960 | 1WXS | 10 | 83 | 0.038285546366651275 | -0.034654296629024806 | 0.529 | 0.681 |
91
+ | P62166 | 2LCP | 20 | 190 | 0.2098308598721936 | 0.2303096309709702 | 0.316 | 0.613 |
92
+ | P62826 | 2MMC | 10 | 216 | 0.3406053894425987 | 0.16715607473296895 | 0.432 | 0.744 |
93
+ | P62937 | 1OCA | 20 | 165 | 0.1284000748003099 | -0.04492827184569765 | 0.182 | 0.508 |
94
+ | P62993 | 1AZE | 10 | 54 | 0.41574232894987606 | 0.6319420621307412 | 0.364 | 0.748 |
95
+ | P63000 | 2RMK | 25 | 191 | 0.22975682006062276 | 0.15284341416368147 | 0.282 | 0.532 |
96
+ | P63096 | 5JS7 | 10 | 321 | 0.0737490567132989 | 0.01336637255471063 | 0.338 | 0.619 |
97
+ | P63172 | 5JPW | 20 | 113 | -0.04565340342005457 | -0.014438751746623197 | 0.043 | 0.479 |
98
+ | P68036 | 6N13 | 10 | 151 | 0.3984071104914604 | 0.4223387940048797 | 0.452 | 0.738 |
99
+ | P68871 | 2H35 | 20 | 146 | 0.0981924749115518 | -0.035531605178679884 | 0.200 | 0.527 |
100
+ | P80511 | 2M9G | 20 | 92 | 0.6444369095140483 | 0.5646779587873556 | 0.421 | 0.765 |
101
+ | P83876 | 1PQN | 20 | 127 | 0.3648293963254593 | 0.22558117735283087 | 0.308 | 0.628 |
102
+ | P84077 | 1U81 | 11 | 164 | 0.10317630895215811 | 0.10585882769034045 | 0.212 | 0.645 |
103
+ | P99999 | 1J3S | 20 | 104 | 0.3476261602475195 | 0.36032220206977494 | 0.429 | 0.666 |
104
+ | Q01469 | 1JJJ | 20 | 133 | 0.3554136358535416 | 0.024688587139490514 | 0.148 | 0.513 |
105
+ | Q06141 | 2GO0 | 20 | 137 | 0.4271006403195997 | 0.18742882744973585 | 0.536 | 0.822 |
106
+ | Q07812 | 1F16 | 20 | 192 | 0.435395925453707 | 0.34680268833247435 | 0.410 | 0.751 |
107
+ | Q07817 | 2LP8 | 21 | 169 | 0.4702898911043708 | 0.3703868529660385 | 0.294 | 0.644 |
108
+ | Q12824 | 5AJ1 | 20 | 112 | 0.26300953292103735 | 0.11039737588410156 | 0.217 | 0.511 |
109
+ | Q13404 | 2HLW | 15 | 140 | 0.3632503116048196 | 0.04930572259517615 | 0.429 | 0.709 |
110
+ | Q15369 | 2MA9 | 20 | 91 | -0.12025800286669854 | 0.004873387482083134 | 0.053 | 0.385 |
111
+ | Q15370 | 2JZ3 | 20 | 118 | -0.1599122047776086 | -0.21364843199339711 | 0.083 | 0.310 |
112
+ | Q15843 | 2KO3 | 20 | 76 | 0.3061107313738893 | 0.12880382775119617 | 0.375 | 0.725 |
113
+ | Q16539 | 2LGC | 10 | 354 | -0.11521271480614616 | -0.15701408721208995 | 0.141 | 0.438 |
114
+ | Q16611 | 2M5B | 20 | 169 | 0.06931032768136841 | -0.23356869374968925 | 0.235 | 0.497 |
115
+ | Q86Y78 | 6IB6 | 20 | 95 | 0.10062989921612542 | -0.24125139977603582 | 0.105 | 0.413 |
116
+ | Q8WXC3 | 2HM2 | 20 | 89 | 0.0955056179775281 | -0.09055158324821247 | 0.222 | 0.544 |
117
+ | Q92843 | 1MK3 | 10 | 168 | 0.39999544444500695 | 0.40199988864198916 | 0.471 | 0.824 |
118
+ | Q92882 | 1X2K | 20 | 55 | 0.1147907647907648 | 0.061183261183261194 | 0.273 | 0.531 |
119
+ | Q95460 | 7RNO | 10 | 244 | -0.10809676633251963 | 0.009993845747163466 | 0.143 | 0.504 |
120
+ | Q969V5 | 6K2K | 20 | 56 | 0.1382775119617225 | 0.3856459330143541 | 0.417 | 0.714 |
121
+ | Q96B02 | 2MT6 | 20 | 151 | 0.4017706517950505 | 0.1610596026490066 | 0.581 | 0.820 |
122
+ | Q96PM5 | 2JRJ | 20 | 51 | 0.5485067873303168 | 0.5841628959276017 | 0.545 | 0.691 |
123
+ | Q99963 | 2EW3 | 10 | 60 | 0.14554042789663796 | 0.2208946929702696 | 0.250 | 0.530 |
124
+ | Q9BTP7 | 2LYH | 20 | 75 | 0.4328022759601707 | 0.35206258890469416 | 0.467 | 0.830 |
125
+ | Q9BXW4 | 2NCN | 10 | 126 | 0.2175178102737158 | 0.17849268841394828 | 0.115 | 0.425 |
126
+ | Q9GZQ8 | 2LUE | 20 | 115 | -0.11907993371735186 | -0.13845182671821984 | 0.217 | 0.396 |
127
+ | Q9HC16 | 2JYW | 10 | 182 | 0.4627477404399784 | 0.34420854935301093 | 0.405 | 0.695 |
128
+ | Q9HD47 | 5YFG | 20 | 186 | 0.21704889295022123 | 0.23889616716941195 | 0.263 | 0.649 |
129
+ | Q9NYG5 | 2MT5 | 20 | 68 | -0.18364698247890976 | 0.0071763942436156814 | 0.214 | 0.398 |
130
+ | Q9NZ01 | 2DZJ | 20 | 81 | -0.10033875338753388 | -0.16095302619692864 | 0.353 | 0.456 |
131
+ | Q9NZQ7 | 6L8R | 20 | 31 | 0.7254032258064517 | 0.6419354838709678 | 0.571 | 0.929 |
132
+ | Q9UHA7 | 6HPI | 20 | 158 | 0.5772447019056558 | 0.45845420843100954 | 0.531 | 0.791 |
133
+ | Q9Y295 | 2EKI | 20 | 80 | -0.022456633849038912 | 0.21776840131270514 | 0.062 | 0.495 |
134
+ | Q9Y320 | 2DJ0 | 20 | 124 | 0.2645476003147128 | 0.19507159716758457 | 0.160 | 0.544 |
135
+ | Q9Y547 | 1XPW | 20 | 143 | 0.38667963491907154 | 0.3015488033093667 | 0.276 | 0.666 |
confidence_conformation_v5/rmsf_calibration_1289.json ADDED
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confidence_conformation_v5/rmsf_calibration_1289.md ADDED
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1
+ # AF2-RMSF Experimental Ensemble Calibration
2
+
3
+ - Verdict: `rank_only`
4
+ - Calibrated proteins: 121
5
+ - Median Spearman: 0.21704889295022123
6
+ - Median partial Spearman controlling 1-pLDDT: 0.14851839694428695
7
+ - Median top-20% recall: 0.3076923076923077
8
+ - Median flexible-region AUROC: 0.627951256664128
9
+ - Annotated-IDP subset: {'n_proteins': 19, 'median_spearman': 0.16504242848394715, 'median_top20_recall': 0.26666666666666666, 'median_flexible_auc': 0.5802103879026956, 'median_uncertainty_spearman': -0.060834692788680665, 'median_partial_spearman': 0.21536240205703797, 'median_spearman_ci95': [-0.17145721925133692, 0.41574232894987606], 'median_top20_recall_ci95': [0.1724137931034483, 0.4117647058823529], 'median_flexible_auc_ci95': [0.4690265486725664, 0.7205882352941176], 'median_partial_spearman_ci95': [0.001501885448866303, 0.248346590118742], 'verdict': 'rank_only'}
10
+ - Important limitation: deposited NMR models are restraint-compatible ensembles, not Boltzmann-weighted trajectories.
11
+ - MSA-depth confounding is not measured because the source LMDB does not retain MSA depth.
12
+
13
+ | UniProt | PDB | Models | Residues | Spearman | Partial | Top20 | AUROC |
14
+ |---|---:|---:|---:|---:|---:|---:|---:|
15
+ | A1B602 | 2LL0 | 20 | 104 | -0.3571001813720261 | 0.12300224047796865 | 0.000 | 0.194 |
16
+ | A5Y0M2 | 7DFE | 10 | 142 | 0.14132915331596785 | 0.21536240205703797 | 0.172 | 0.469 |
17
+ | A8AZZ3 | 2MXX | 20 | 171 | 0.5731994144046849 | 0.5311709506323951 | 0.571 | 0.870 |
18
+ | C9ZXG5 | 2MXN | 20 | 142 | 0.5305737115746106 | 0.45626384403729325 | 0.724 | 0.845 |
19
+ | D6PZY5 | 4C7Q | 20 | 85 | 0.42071526284932576 | 0.2395348837209302 | 0.412 | 0.721 |
20
+ | E9AD06 | 2M5R | 20 | 78 | 0.2828184473754094 | 0.248346590118742 | 0.188 | 0.649 |
21
+ | G1K3N3 | 2LC2 | 20 | 108 | 0.6861966141739785 | 0.41577829222517554 | 0.409 | 0.847 |
22
+ | G8HXD9 | 2LFW | 15 | 56 | 0.6019822282980178 | 0.23451811346548188 | 0.667 | 0.790 |
23
+ | O00244 | 1TL4 | 30 | 68 | 0.378134900942856 | 0.07939840439745009 | 0.571 | 0.734 |
24
+ | O14618 | 2CRL | 20 | 86 | 0.6742110476909289 | 0.12599650926930517 | 0.500 | 0.819 |
25
+ | O14893 | 2LEH | 32 | 186 | 0.6115157420660267 | 0.44113684151634813 | 0.342 | 0.773 |
26
+ | O14907 | 2KG2 | 20 | 123 | 0.38928299647882786 | 0.3135584475887065 | 0.440 | 0.722 |
27
+ | O14933 | 2KJH | 16 | 150 | 0.19202453442375217 | 0.22561536068269702 | 0.233 | 0.564 |
28
+ | O43819 | 2RLI | 31 | 167 | 0.4262086841806921 | 0.1402779638657281 | 0.412 | 0.699 |
29
+ | O75365 | 1R6H | 20 | 169 | 0.5448063248968228 | 0.3865695390582269 | 0.471 | 0.685 |
30
+ | O75771 | 2KZ3 | 20 | 83 | 0.09487427060157004 | 0.18116367910667058 | 0.118 | 0.577 |
31
+ | O95166 | 1KLV | 20 | 100 | 0.45202520252025197 | 0.2655385538553855 | 0.500 | 0.604 |
32
+ | O95881 | 2K8V | 40 | 149 | 0.5084745147832396 | 0.35463450027208415 | 0.400 | 0.695 |
33
+ | P00374 | 1YHO | 25 | 186 | 0.20875196397018028 | 0.303386187636662 | 0.395 | 0.684 |
34
+ | P00441 | 1BA9 | 36 | 148 | 0.19369060883921865 | 0.06050633567412091 | 0.167 | 0.596 |
35
+ | P01034 | 6RPV | 20 | 119 | 0.11714143284432418 | 0.1290129611166501 | 0.167 | 0.468 |
36
+ | P01215 | 1DZ7 | 27 | 92 | -0.03722084367245657 | -0.004700769076645654 | 0.105 | 0.373 |
37
+ | P02649 | 1OEF | 5 | 24 | 0.12347826086956522 | 0.04347826086956521 | 0.600 | 0.653 |
38
+ | P03950 | 1AWZ | 30 | 123 | 0.31921424978395735 | 0.23658278624034257 | 0.480 | 0.767 |
39
+ | P04083 | 1BO9 | 21 | 73 | 0.32006664198445023 | 0.3088670862643466 | 0.467 | 0.756 |
40
+ | P04439 | 6MPP | 10 | 259 | 0.14270750451518296 | 0.017338261698104273 | 0.288 | 0.633 |
41
+ | P04637 | 1DT7 | 40 | 22 | -0.4116318464144552 | -0.28514963297572 | 0.200 | 0.259 |
42
+ | P05112 | 1BCN | 22 | 127 | 0.22355994563179601 | -0.19875445256842894 | 0.308 | 0.641 |
43
+ | P05231 | 2IL6 | 32 | 166 | -0.17383895953984696 | -0.08241436076368623 | 0.118 | 0.249 |
44
+ | P05412 | 1JUN | 7 | 39 | -0.7163967611336033 | -0.6384615384615385 | 0.000 | 0.113 |
45
+ | P05452 | 1RJH | 20 | 117 | 0.2560505926958294 | 0.4104437351076743 | 0.375 | 0.573 |
46
+ | P06702 | 5I8N | 10 | 113 | 0.5331109854281723 | -0.03429203539823009 | 0.739 | 0.936 |
47
+ | P06703 | 2M1K | 20 | 88 | 0.6698601669543166 | 0.5188968335035752 | 0.500 | 0.842 |
48
+ | P06730 | 2GPQ | 10 | 217 | 0.22516875942445638 | -0.07167049516857152 | 0.295 | 0.603 |
49
+ | P06748 | 2LLH | 20 | 70 | 0.16504242848394715 | 0.5857930189834659 | 0.286 | 0.495 |
50
+ | P06899 | 2RVQ | 10 | 126 | 0.4280374953130859 | 0.4586936632920885 | 0.423 | 0.786 |
51
+ | P07305 | 6HQ1 | 20 | 74 | 0.27460940392447236 | 0.23465383191410583 | 0.267 | 0.641 |
52
+ | P07737 | 1PFL | 20 | 139 | 0.14278117878368113 | 0.07430180079538852 | 0.179 | 0.456 |
53
+ | P07910 | 1TXP | 20 | 27 | -0.4975579975579975 | -0.4554334554334554 | 0.000 | 0.143 |
54
+ | P07998 | 2K11 | 20 | 127 | 0.24889271653543305 | 0.22090012185976754 | 0.577 | 0.732 |
55
+ | P08034 | 5KK9 | 20 | 21 | -0.5194805194805194 | -0.6090909090909091 | 0.200 | 0.287 |
56
+ | P09651 | 2LYV | 20 | 195 | -0.011207496479955979 | 0.001501885448866303 | 0.154 | 0.580 |
57
+ | P09936 | 2LEN | 20 | 222 | 0.07737825279371047 | 0.11693468116575478 | 0.222 | 0.485 |
58
+ | P10415 | 8U27 | 20 | 165 | 0.47792589426441917 | 0.4950418080303476 | 0.424 | 0.728 |
59
+ | P10599 | 1CQG | 35 | 100 | 0.39157515751575156 | 0.23488748874887486 | 0.450 | 0.799 |
60
+ | P14174 | 8CA0 | 4 | 114 | 0.1754966485085357 | 0.12648184524412223 | 0.261 | 0.609 |
61
+ | P15309 | 2L3H | 8 | 39 | -0.018218623481781375 | 0.007085020242914981 | 0.250 | 0.496 |
62
+ | P16220 | 2LXT | 20 | 33 | -0.17145721925133692 | -0.0945855614973262 | 0.429 | 0.434 |
63
+ | P18510 | 1IRP | 12 | 152 | 0.23314128718758326 | 0.10105317832954024 | 0.226 | 0.541 |
64
+ | P20472 | 1RJV | 19 | 110 | 0.11157496111624551 | 0.013105515857809436 | 0.364 | 0.673 |
65
+ | P21730 | 2K3U | 25 | 20 | -0.35939849624060144 | -0.21353383458646616 | 0.250 | 0.391 |
66
+ | P21796 | 2K4T | 20 | 283 | 0.5063703777434927 | 0.4227845836011482 | 0.333 | 0.704 |
67
+ | P23297 | 2L0P | 20 | 93 | 0.21658559875861652 | 0.14851839694428695 | 0.474 | 0.678 |
68
+ | P23396 | 1WH9 | 20 | 79 | -0.1785053554040896 | -0.23264362220058424 | 0.250 | 0.384 |
69
+ | P26447 | 1M31 | 20 | 101 | 0.6716715200931858 | 0.7165637740244611 | 0.667 | 0.898 |
70
+ | P26992 | 1UC6 | 21 | 103 | -0.13791020515749242 | -0.20854017484514342 | 0.000 | 0.440 |
71
+ | P29033 | 5KJ3 | 20 | 22 | -0.13382269904009036 | -0.0378317334839074 | 0.000 | 0.188 |
72
+ | P32881 | 6JHD | 15 | 166 | 0.5898393792917999 | 0.42173396908264527 | 0.500 | 0.819 |
73
+ | P33763 | 2KAX | 31 | 92 | 0.6792380130388546 | 0.4286176656443136 | 0.526 | 0.890 |
74
+ | P35414 | 2LOT | 40 | 55 | 0.5257575757575759 | -0.0546897546897547 | 0.545 | 0.750 |
75
+ | P35613 | 5XF0 | 20 | 107 | -0.1687924920159094 | -0.06864358627716059 | 0.045 | 0.425 |
76
+ | P37235 | 5T7C | 10 | 185 | 0.20576930366551682 | 0.19398051628065655 | 0.324 | 0.571 |
77
+ | P37802 | 1WYM | 20 | 142 | 0.4652413813336798 | 0.31792091636263053 | 0.276 | 0.724 |
78
+ | P37840 | 2KKW | 34 | 140 | -0.3072139249087053 | -0.1366206730664101 | 0.143 | 0.494 |
79
+ | P41159 | 8K6Z | 10 | 146 | -0.20045887036912075 | -0.18965806445393465 | 0.100 | 0.282 |
80
+ | P43897 | 2CP9 | 20 | 52 | 0.4559890719713139 | 0.4657218475198497 | 0.545 | 0.763 |
81
+ | P49795 | 1CMZ | 20 | 128 | 0.07169588903131294 | 0.09658830800219739 | 0.308 | 0.616 |
82
+ | P51681 | 6FGP | 10 | 24 | -0.09391304347826085 | 0.013913043478260868 | 0.200 | 0.474 |
83
+ | P51809 | 2DMW | 20 | 117 | -0.0005245095835393907 | -0.0835618696518755 | 0.458 | 0.560 |
84
+ | P52565 | 2N80 | 10 | 174 | -0.4450821492639312 | -0.32363449984338954 | 0.057 | 0.170 |
85
+ | P55000 | 6ZZE | 20 | 81 | 0.19911924119241192 | 0.15259710930442638 | 0.118 | 0.481 |
86
+ | P56278 | 1QTT | 20 | 107 | 0.5325927232116617 | 0.16265992672270224 | 0.591 | 0.835 |
87
+ | P57730 | 1DGN | 20 | 89 | 0.45240040858018393 | 0.42521280217909435 | 0.556 | 0.776 |
88
+ | P60880 | 2N1T | 5 | 74 | -0.22416882636060712 | -0.28619029988893 | 0.267 | 0.427 |
89
+ | P61769 | 1JNJ | 20 | 99 | 0.15628942486085343 | -0.004650587507730364 | 0.300 | 0.647 |
90
+ | P61960 | 1WXS | 10 | 83 | 0.038285546366651275 | -0.034654296629024806 | 0.529 | 0.681 |
91
+ | P62166 | 2LCP | 20 | 190 | 0.2098308598721936 | 0.2303096309709702 | 0.316 | 0.613 |
92
+ | P62826 | 2MMC | 10 | 216 | 0.3406053894425987 | 0.16715607473296895 | 0.432 | 0.744 |
93
+ | P62937 | 1OCA | 20 | 165 | 0.1284000748003099 | -0.04492827184569765 | 0.182 | 0.508 |
94
+ | P62993 | 1AZE | 10 | 54 | 0.41574232894987606 | 0.6319420621307412 | 0.364 | 0.748 |
95
+ | P63000 | 2RMK | 25 | 191 | 0.22975682006062276 | 0.15284341416368147 | 0.282 | 0.532 |
96
+ | P63096 | 5JS7 | 10 | 321 | 0.0737490567132989 | 0.01336637255471063 | 0.338 | 0.619 |
97
+ | P63172 | 5JPW | 20 | 113 | -0.04565340342005457 | -0.014438751746623197 | 0.043 | 0.479 |
98
+ | P68036 | 6N13 | 10 | 151 | 0.3984071104914604 | 0.4223387940048797 | 0.452 | 0.738 |
99
+ | P68871 | 2H35 | 20 | 146 | 0.0981924749115518 | -0.035531605178679884 | 0.200 | 0.527 |
100
+ | P80511 | 2M9G | 20 | 92 | 0.6444369095140483 | 0.5646779587873556 | 0.421 | 0.765 |
101
+ | P83876 | 1PQN | 20 | 127 | 0.3648293963254593 | 0.22558117735283087 | 0.308 | 0.628 |
102
+ | P84077 | 1U81 | 11 | 164 | 0.10317630895215811 | 0.10585882769034045 | 0.212 | 0.645 |
103
+ | P99999 | 1J3S | 20 | 104 | 0.3476261602475195 | 0.36032220206977494 | 0.429 | 0.666 |
104
+ | Q01469 | 1JJJ | 20 | 133 | 0.3554136358535416 | 0.024688587139490514 | 0.148 | 0.513 |
105
+ | Q06141 | 2GO0 | 20 | 137 | 0.4271006403195997 | 0.18742882744973585 | 0.536 | 0.822 |
106
+ | Q07812 | 1F16 | 20 | 192 | 0.435395925453707 | 0.34680268833247435 | 0.410 | 0.751 |
107
+ | Q07817 | 2LP8 | 21 | 169 | 0.4702898911043708 | 0.3703868529660385 | 0.294 | 0.644 |
108
+ | Q12824 | 5AJ1 | 20 | 112 | 0.26300953292103735 | 0.11039737588410156 | 0.217 | 0.511 |
109
+ | Q13404 | 2HLW | 15 | 140 | 0.3632503116048196 | 0.04930572259517615 | 0.429 | 0.709 |
110
+ | Q15369 | 2MA9 | 20 | 91 | -0.12025800286669854 | 0.004873387482083134 | 0.053 | 0.385 |
111
+ | Q15370 | 2JZ3 | 20 | 118 | -0.1599122047776086 | -0.21364843199339711 | 0.083 | 0.310 |
112
+ | Q15843 | 2KO3 | 20 | 76 | 0.3061107313738893 | 0.12880382775119617 | 0.375 | 0.725 |
113
+ | Q16539 | 2LGC | 10 | 354 | -0.11521271480614616 | -0.15701408721208995 | 0.141 | 0.438 |
114
+ | Q16611 | 2M5B | 20 | 169 | 0.06931032768136841 | -0.23356869374968925 | 0.235 | 0.497 |
115
+ | Q86Y78 | 6IB6 | 20 | 95 | 0.10062989921612542 | -0.24125139977603582 | 0.105 | 0.413 |
116
+ | Q8WXC3 | 2HM2 | 20 | 89 | 0.0955056179775281 | -0.09055158324821247 | 0.222 | 0.544 |
117
+ | Q92843 | 1MK3 | 10 | 168 | 0.39999544444500695 | 0.40199988864198916 | 0.471 | 0.824 |
118
+ | Q92882 | 1X2K | 20 | 55 | 0.1147907647907648 | 0.061183261183261194 | 0.273 | 0.531 |
119
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confidence_conformation_v5/rmsf_calibration_entities.json ADDED
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