MakeTNT-toolkit User Documentation | To MakeTNT-manual |
MakeTNT Evaluation |
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[1] | From the first 50000 compounds of the NCI open source database, 49967 structures with 3D coordinates have been selected. 10 of the structures have kindly been provided by Dr. Armin Ruf, Roche, Basel. XPLOR-type *.top and *.par files have been obtained from Corina. |
[2] | All 2457 cif monomer descriptions (ccp4-4.2.2) have been run through Libcheck, Vers 4.0.1. 2426 lib-files could be obtained. For 31 files Libcheck failed. |
[3] | From the first 20000 compounds of the NCI open source database, 3289 compounds have been selected if they had 3D coordinates and fulfilled at least one of the following criteria: > 1 4-atom ring, > 2 5-atom rings, > 2 6-atom rings, > 4 (4-6)-atom rings. |
[4] | Compounds including metal atoms can cause trouble, as metal coordination is treated as a covalent bond by xplo2d, which increases the number of ring systems to be processed by MakeTNT. In order to cope with this problem, MakeTNT has been configured to process generous numbers of ring systems. In case of problems, please make sure, that the metal coordination listed in the *.top files generated by xplo2d is correct. If it still does not work, let us know. |
[5] | The test was run on Refmac-dictionaries generated by Corina for the first 1000 coordinates of the NCI-dataset. |
compound number of atoms |
structure | optimisation: jiggle[Å]/Size of
MakeTNT-Restraint file no. refinement cycles/successful? |
||||||||
0.25/s | 0.25/m | 0.25/l | 0.5/s | 0.5/m | 0.5/l | 1.0/s | 1.0/m | 1.0/l | ||
---|---|---|---|---|---|---|---|---|---|---|
NCI124652/28 | 126 yes[a] |
57 yes[a] |
74 yes[a] |
49 yes[a] |
45 yes[a] |
167 yes[a] |
73 yes[a] |
108 yes[a] |
55 no |
|
NIST04051410392D/10 | 16 yes |
36 yes |
17 yes |
17 yes |
81 yes |
14 yes |
36 yes |
32 yes |
29 yes |
|
NCI16498/25 | 13 yes |
16 yes |
184 yes |
17 yes |
25 yes |
86 yes |
60 yes |
88 yes |
114 yes |
|
NCI367798/48 | 116 yes |
231 yes |
494 yes |
284 yes |
219 yes |
>2001 no |
98 yes |
416 no |
415 no |
|
NCI376722/29 | 26 yes[a] |
21 yes[a] |
144 yes[a] |
18 yes[a] |
26 yes[a] |
62 yes[a] |
158 yes[a] |
205 yes[a] |
415 no |
|
NCI46/20 | 46 yes |
21 yes |
21 yes |
59 yes |
117 yes |
215 yes |
72 yes |
136 yes |
243 yes |
|
NCI56940/28 | 21 yes |
134 yes |
173 yes |
21 yes |
74 yes |
173 yes |
73 yes |
258 yes |
115 yes |
|
NCI628503/58 | 147 yes |
127 yes |
140 yes |
190 yes |
151 yes |
396 no |
238 yes |
223 no |
624 no |
|
NCI631303/29 | 21 yes |
46 yes |
88 yes |
199 yes |
25 yes |
189 no |
35 yes |
131 yes |
303 no |
|
NCI640266/26 | 61 yes |
72 yes |
157 yes |
31 yes |
75 yes |
125 yes |
112 yes |
127 yes |
266 yes |
[a]: structure of good quality, except for positioning of metal ions(e.g. Cu, Co), where currently no parameters for non-bonded interactions are available in Buster/TNT
compound number of atoms |
structure | optimisation: jiggle [Å] / Size of
MakeTNT-Restraint file no. refinement cycles / successful? |
|||||
0.25/s | 0.25/l | 0.5/s | 0.5/l | 1.0/s | 1.0/l | ||
---|---|---|---|---|---|---|---|
AQS 28 |
16 yes |
13 yes |
30 yes |
40 yes |
30 yes |
46 yes |
|
BRL 25 |
28 yes |
55 yes |
36 yes |
34 yes |
45 yes |
36 yes |
|
DPS 36 |
55 yes |
93 yes |
24 yes |
106 yes |
100 yes |
291 yes |
|
EST 20 |
36 yes |
24 yes |
53 yes |
29 yes |
90 no |
86 yes |
|
GR3 39 |
73 no |
96 no |
73 no |
294 no |
169 no |
529 no |
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MTB 22 |
no atom labels in Refmac input (e.g.: 'C5'') currently not recognized by TNT |
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NEV 20 |
80 yes |
34 yes |
102 yes |
71 yes |
106 yes |
29 yes |
|
TMF 33 |
40 yes |
105 yes |
72 no |
56 yes |
99 yes |
136 no |
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TXL 58 |
225 yes |
257 yes |
206 yes |
155 no |
395 yes |
273 no |
|
ZYA 28 |
56 yes |
22 yes |
95 yes |
44 yes |
61 yes |
71 yes |