MakeTNT-toolkit User Documentation | To MakeTNT-manual |
MDL2TNT/PDB2TNT Evaluation |
Source of compounds | Number of compounds | Successful Generation of Restraints | Failures |
---|---|---|---|
NCI diversity data set | 1990 | 1990 | - |
The bond recognition algorithm of PDB2TNT has been tested using 3D-coordinates (but not the bond table !!) from the NCI diversity data set and bond-restraints generated this way have been compared to the ones obtained by MDL2TNT (with explicit knowledge of bond orders). Results are shown below:
Source of compounds | Number of compounds | Number of structures with fully correct bond restraints | Number of structures with missing bonds | Number of structures with too many bonds | Reasons for additional bonds |
---|---|---|---|---|---|
NCI diversity data set | 1990 | 1970 | - | 20 |
|
Recognition of planar restraints by PDB2TNT has been tested by comparing planar restraints (format:s) obtained by its hybridisation-determining algorithm to the ones obtained from MDL2TNT. 2 test runs have been performed: one including the positions of H-atoms and one without knowledge of H-atom positions. Manual inspection of discrepancies between MDL-file and PDB-file derived restraints indicated that:
Source of compounds | Number of compounds | Inclusion of H-positions | Differences between MDL- and PDB-derived restraints | Reason for differences: | |
---|---|---|---|---|---|
NCI
diversity data set 3D-MDL-files |
1990 | yes | 34 |
|
|
NCI
diversity data set 3D-MDL-files |
1990 | no | 83 |
|
Initial coordinates (with the correct stereochemistry around asymmetric centers) have been randomized to RMS deviations of 0.5 and 1.0 Ångstrøms and optimized with TNT-dictionaries, sizes m and l, derived either from a 3D-mdl file (M) or a PDB-file (P). For example, 0.5/m/M means, the compound has been distorted to an initial RMSD of 0.5Ångstrøms, optimized with a TNT-dictionary file of size m derived from a 3D-MDL file.
Optimizations producing apparent errors in the geometry have been marked in red. The results indicate that:
compound number of atoms |
structure | optimisation: jiggle[Å]/Size of
-Restraint file/Source M:MDL2TNT; P:PDB2TNT no. refinement cycles/successful? |
|||||||
0.5/m/M | 0.5/s/M | 0.5/m/P | 0.5/s/P | 1.0/m/M | 1.0/s/M | 1.0/m/P | 1.0/s/P | ||
NCI124652/28 | 98 yes[a] |
116 yes[a] |
83 yes[a] |
40 yes[a] |
91 yes[a] |
101 no |
98 yes[a] |
71 no |
|
NIST04051410392D/10 | 36 yes |
36 yes |
45 yes |
45 yes |
50 yes |
50 yes |
106 yes |
106 yes |
|
NCI16498/25 | 44 yes |
79 yes |
56 yes |
46 yes |
80 yes |
71 yes |
79 yes |
48 yes |
|
NCI367798/48 | 120 yes |
267 yes |
115 yes |
87 yes |
115 yes |
215 yes |
91 yes |
113 yes |
|
NCI376722/29 | 96 yes[a] |
98 yes[a] |
75 yes[a] |
58 yes[a] |
101 yes[a] |
156 yes[a] |
102 yes[a] |
91 yes[a] |
|
NCI46/20 | 65 yes |
107 yes |
77 yes |
92 yes |
92 yes |
148 no |
103 yes |
91 no |
|
NCI56940/28 | 84 yes |
98 yes |
87 yes |
63 yes |
105 yes |
116 yes |
124 yes |
104 no |
|
NCI628503/58 | 104 yes |
118 yes |
81 yes |
101 yes |
109 yes |
1091 no |
115 yes |
323 no |
|
NCI631303/29 | 80 yes |
154 yes |
89 yes |
78 yes |
76 yes |
91 yes |
96 yes |
113 yes |
|
NCI640266/26 | 152 yes |
78 yes |
154 yes |
57 yes |
132 yes |
73 yes |
158 yes |
79 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