Datasets » History » Version 10

Anonymous, 04/11/2008 12:20 PM

1 1 Anonymous
= Datasets =
2 1 Anonymous
3 1 Anonymous
== How to label datasets ==
4 1 Anonymous
Datasets are labeled in the following way:
5 1 Anonymous
{{{
6 1 Anonymous
DatasetName.tgz
7 1 Anonymous
DatasetName_Literature.tgz
8 1 Anonymous
DatasetName_NumberOfChains_Extraction.tgz
9 1 Anonymous
}}}
10 1 Anonymous
11 1 Anonymous
whereas:
12 1 Anonymous
 || '''!DatasetName'''     || Authors or web that site proposed the dataset
13 1 Anonymous
 || '''Literature'''       || Special name given in the literatur
14 1 Anonymous
 || '''!NumberOfChains'''  || Number of (extracted) chains contained in the dataset
15 1 Anonymous
 || '''Extraction'''       || Extraction of the models/chains: ''none'', ''first-first'', ''first-all'', ''all-all''
16 1 Anonymous
17 1 Anonymous
== Available Datasets ==
18 1 Anonymous
The following datasets are available from the repository (special privileges required!):
19 1 Anonymous
 || '''!DatasetName'''      || '''Extraction'''   || '''!NumberOfChains''' || '''Size in MB''' || '''Link''' 
20 1 Anonymous
 || !LelukKoniecznyRoterman || -            || -               || 3.5        || [source:Datasets/LelukKoniecznyRoterman.tgz Download]
21 1 Anonymous
 ||                         || first-first  || 6               || 0.4        || [source:Datasets/LelukKoniecznyRoterman_6_first-first.tgz Download]
22 1 Anonymous
 ||                         || first-all    || 15              || 0.9        || [source:Datasets/LelukKoniecznyRoterman_15_first-all.tgz Download]
23 1 Anonymous
24 1 Anonymous
 || '''!DatasetName'''      || '''Extraction'''   || '''!NumberOfChains''' || '''Size in MB''' || '''Link''' 
25 1 Anonymous
 || !ChewKedem              || -            || -               || 3.8        || [source:Datasets/ChewKedem.tgz Download]
26 1 Anonymous
 ||                         || first-first  || 34              || 1.3        || [source:Datasets/ChewKedem_34_first-first.tgz Download]
27 1 Anonymous
 ||                         || first-all    || 54              || 2.0        || [source:Datasets/ChewKedem_54_first-all.tgz Download]
28 1 Anonymous
 ||                         || all-all      || 132             || 4.1        || [source:Datasets/ChewKedem_132_all-all.tgz Download]
29 1 Anonymous
30 1 Anonymous
 || '''!DatasetName'''      || '''Extraction'''   || '''!NumberOfChains''' || '''Size in MB''' || '''Link''' 
31 1 Anonymous
 || !ProteinKinaseResource  || -            || -               || 3.6        || [source:Datasets/ProteinKinaseResource.tgz Download]
32 1 Anonymous
 ||                         || first-first  || 45              || 2.4        || [source:Datasets/ProteinKinaseResource_45_first-first.tgz Download]
33 1 Anonymous
 ||                         || first-all    || 49              || 2.5        || [source:Datasets/ProteinKinaseResource_49_first-all.tgz Download]
34 1 Anonymous
 ||                         || all-all      || 106             || 4.0        || [source:Datasets/ProteinKinaseResource_106_all-all.tgz Download]
35 1 Anonymous
36 1 Anonymous
 || '''!DatasetName'''      || '''Extraction'''   || '''!NumberOfChains''' || '''Size in MB''' || '''Link''' 
37 1 Anonymous
 || Skolnick                || -            || -               || 5.1        || [source:Datasets/Skolnick.tgz Download]
38 1 Anonymous
 ||                         || first-first  || 33              || 1.1        || [source:Datasets/Skolnick_33_first-first.tgz Download]
39 1 Anonymous
 ||                         || first-all    || 65              || 2.1        || [source:Datasets/Skolnick_65_first-all.tgz Download]
40 1 Anonymous
 ||                         || all-all      || 179             || 5.9        || [source:Datasets/Skolnick_179_all-all.tgz Download]
41 1 Anonymous
42 1 Anonymous
 || '''!DatasetName'''      || '''Extraction'''   || '''!NumberOfChains''' || '''Size in MB''' || '''Link''' 
43 1 Anonymous
 || !RostSander             || -            || -               || 7.4        || [source:Datasets/RostSander.tgz Download]
44 1 Anonymous
 ||                         || RS126        || 126             || 4.3        || [source:Datasets/RostSander_RS126.tgz Download]
45 1 Anonymous
 ||                         || first-first  || 119             || 4.4        || [source:Datasets/RostSander_119_first-first.tgz Download]
46 1 Anonymous
 ||                         || first-all    || 212             || 7.6        || [source:Datasets/RostSander_212_first-all.tgz Download]
47 1 Anonymous
48 1 Anonymous
 || '''!DatasetName'''            || '''Extraction'''   || '''!NumberOfChains''' || '''Size in MB''' || '''Link''' 
49 1 Anonymous
 || !KinjoHorimotoNishikawa || -            || -               || 98         || [source:Datasets/KinjoHorimotoNishikawa.tgz Download]
50 1 Anonymous
 ||                         || first-first  || 1012            || 46         || [source:Datasets/KinjoHorimotoNishikawa_1012_first-first.tgz Download]
51 1 Anonymous
 ||                         || first-all    || 2013            || 88         || [source:Datasets/KinjoHorimotoNishikawa_2013_first-all.tgz Download]
52 2 Anonymous
53 4 Anonymous
 || '''!DatasetName'''  || '''Description'''          || '''Extraction type / time'''   || '''!NumberOfChains''' || '''Size in MB'''         || '''Link''' 
54 5 Anonymous
 || Shah1                || Randomly selected 1000 proteins from PDB     || -            || -               || 114         || [source:Datasets/Shah.tgz Download]                   
55 4 Anonymous
 ||                     ||                            || first-first  || 1000            || 41          || [source:Datasets/Shah_1000_first-first.tgz Download]
56 4 Anonymous
 ||                     ||                            || first-all    || 1943            || 80          || [source:Datasets/Shah_1943_first-all.tgz Download]
57 1 Anonymous
 ||                     ||                            || all-all      || 4007            || 124         || [source:Datasets/Shah_4007_all-all.tgz Download]
58 5 Anonymous
59 5 Anonymous
60 7 Anonymous
 || '''!DatasetName'''  || '''Description'''          || '''Extraction type / time'''   || '''!NumberOfChains''' || '''Size in GB'''         || '''Link''' 
61 9 Anonymous
 || Shah2               || Downloaded from PDB web site on 10/04/2007               || -            || -               || 1.1,  ucmp*: 4.8         ||                    
62 7 Anonymous
 ||                     || with criteria "Remove similar sequences at 30% identity"           || first-first  || 7307            ||          || 
63 5 Anonymous
 ||                     ||                            || first-all    ||                 ||           || 
64 7 Anonymous
 ||                     ||                            || all-all      ||                 ||          ||  
65 6 Anonymous
66 8 Anonymous
 || '''!DatasetName'''  || '''Description'''          || '''Extraction type / time'''   || '''!NumberOfChains''' || '''Size in GB'''         || '''Link''' 
67 9 Anonymous
 || Shah3               || PDB_SELECT25  as of October2007            || -            || -               || 0.746, ucmp*: 3.4         ||                    
68 10 Anonymous
 ||                     || it's a six monthly updated list of-       || first-first  || 3464            ||0.12,  ucmp*: 0.54,            || 
69 9 Anonymous
 ||                     || non-redundent protein structures                           || first-all    || 8581                || 0.30, ucmp*: 1.4          || 
70 9 Anonymous
 ||                     || Mostly used in Protein Structure Prediction                           || all-all      ||31288                 || 0.854 , ucmp*: 4.1         || 
71 9 Anonymous
72 9 Anonymous
*ucmp: uncompressed