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schwede
ProMod3
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9bdd5401
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9bdd5401
authored
7 years ago
by
Studer Gabriel
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some more info on how the default StructureDB got created
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extras/data_generation/structure_db/README
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@@ -28,3 +28,13 @@ BUT BE AWARE, THE ACCORDING FREQUENCIES IN THE DATABASE WILL BE SET TO 0.0!
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@@ -28,3 +28,13 @@ BUT BE AWARE, THE ACCORDING FREQUENCIES IN THE DATABASE WILL BE SET TO 0.0!
initial database generated in step 2:
initial database generated in step 2:
use assign_structure_profiles.py to perform this task
use assign_structure_profiles.py to perform this task
To qualitatively reproduce the default StructuralDB in ProMod3, you first
perform step 1 and 2 with a non redundant set of protein structures as
defined by PISCES with around 25000 chains (e.g. seq id threshold: 90,
resolution threshold: 2.2).
Repeat step 1 and 2 with a smaller PISCES list (5000-6000 entries,
e.g. seq id threshold: 25 , resolution threshold: 1.8).
The first database serves as default StructureDB and the second db as
the source db for the structural profiles generated in steps 3-5.
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