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You can use the FTrees software for the purpose of aligning two ligands or for finding similar molecules in a database. The following example shows some really good solutions to the given problems.
description : prompt | user commands |  graphic output |  explanation |  program output |
| 1) structural alignment of 1cbx and 7cpa |
| starting FTrees from a shell: |
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local_host:~/dock/flex> ftrees.SunOS |
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(FTrees is a command line driven tool with a hierarchical menu structure) |
| first step : generating the feature trees from mol2 files: |
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FTREES> mol |
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FTREES/MOL> read carboxyptd-a/1cbx_kpl_h |
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FTREES/MOL> draw |
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FTREES/MOL> display |
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FTREES/MOL> generate 1 |
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FTREES> end |
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FTREES> draw 1 n |
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FTREES> display |
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FTREES> mol |
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FTREES/MOL> read carboxyptd-a/7cpa_kpl_h |
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FTREES/MOL> draw |
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FTREES/MOL> display |
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FTREES/MOL> generate 2 |
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FTREES>end |
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FTREES> draw 1 n |
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FTREES> display |
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| second step : comparing the two feature trees: |
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FTREES> compare 0 1 2 y |
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FTREES> drawmat 1 2 y y y |
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FTREES> display |
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| future improvements: comparing multiple feature trees: |
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FTREES> read 1 carboxyptd-a 1 5
>> 5 ftrees loaded from file 'carboxyptd-a'
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FTREES> mtree |
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FTREES> compare 1 5 n n |
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1cbx_k..._kpl_h | 2ctc_k..._kpl_h | 3cpa_k..._kpl_h | \
6cpa_k..._kpl_h | 7cpa_k..._kpl_h ||
0.5175 | 0.8560 || 9 7 | 0 || 9.60 s | 15.0 6 - 12.0 5 \
- 17.0 9 - 33.0 17 - 41.0 20
Process time used: 9.64 s.
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FTREES/MTREES> draw 1 y |
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FTREES/MTREES> display |
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| 2) calculating enrichment factors of ace_structure 16690 |
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FTREES> r 0 ace 18 18 |
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FTREES> r 1 all 1 965
>> 965 ftrees loaded from file 'all'
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FTREES> enrich 1 965 53 87 0 |
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Comparing ftrees 964 of 964
Process time used: 1:53.61 s.
>> Enrich: ace-ST..._16690 || 25.5176 | 19.3994 | 18.5761 | \
15.2670 |13.5858 | 11.2434 | 10.1563 | 9.2055 | 8.4733 | \
7.9743 |
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