Estructuras de proteínas determinadas experimentalmente
|
Fuente* |
Grado de indentidad de la secuencia <= |
Taxon |
Resolución |
Entradas Julio, 2003 |
Entradas Febrero, 2004 |
|
OCA |
sin límite |
todos |
todos (Nota 1) |
22.000 |
25.000 |
|
Represen. |
todos |
" |
5.500 |
5,.00 |
|
|
Sin límite |
Humano (Nota 3) |
" |
4.420 |
4.520 |
|
|
Represen. |
Humano |
" |
1.100 |
1.100 |
|
|
RCSB |
50% |
6.357 |
|||
|
70% |
7.154 |
||||
|
90% |
8.005 |
||||
Redundancia entre estructuras de Proteínas (según RCSB)
|
Search |
entradas |
entradas no redundantes |
Redundant |
|
todos (Note 2) |
24,168 |
6,940 (<50%) |
71% |
|
7,779 (<70%) |
68% |
||
|
8,637 (<90%) |
64% |
||
|
"structural genomics" |
483 |
393 (<70%) |
19% |
|
Deposition before 1980 |
65 |
43 (<70%) |
34% |
|
Deposition 1980-1989 |
434 |
208 (<70%) |
52% |
|
1990-1994 |
2,659 |
952 (<70%) |
64% |
|
Jan 1 - June 10, 1995 |
494 |
282 (<70%) |
43% |
|
1995-1999 |
8,950 |
3,414 (<70%) |
62% |
|
2000-2002 |
9,187 |
4,013 (<70%) |
56% |
|
2003 |
2,642 |
1,435 (<70%) |
46% |
|
Deposition after Sept 15, 2003 (on Feb 7, 2004) |
479 |
331 (<70%) |
31% |
|
Dep. after Aug 10, 2003 (on 2/7/04) and "structure not structural genomics" |
480 |
318 (<70%) |
34% |
|
1980-2004 |
24,085 |
7,751 (<70%) |
68% |
Note 1: At OCA, limiting resolution (e.g. to 3.5 Å) excludes 3,600 NMR results (2/04). These include 860 representative structures, and 240 representative human structures. The exclusion of NMR accounts for the big drop between unlimited resolution (25,000) and 0.1-3.5 Å (20,000); only about 200 entries have resolutions >3.5 Å. Therefore, more accurate results (including both NMR and X-ray) are obtained when a resolution limit is not enforced.
Note 2: At RCSB in July, 2003, one could put "e" in the text query slot to find all entries. This was no longer working in February, 2004. However, one could still find all entries with "deposited after 1970".
(In Feb 2004, due to a bug in OCA, it is important to set the upper date to a week before "today", and request only "released" entries in order to avoid including unreleased entries.)
OCA gives similar results for "human", "homo", or "man". While it was problematic to get a count for human entries at RCSB in early 2003, by 2/04 "human" and "homo" gave similar results in the new (?) "Source" slot. Details follow.
Note 3: OCA (2/04) reports 5,791 for "human", and 5,100 for "homo" or "homo sapiens" or "man" ("Organism" slot). When "man", "homo", or "homo sapiens" is limited to eukaryota, 4,520. "Human" limited to eukaryota gives 4,601. Counts in the table above are for "homo" limited to eukaryota.
At RCSB (2/04):
Source contains "human" gets 4,911 entradas.
Source contains "homo" gets 4,486.
Source contains "homo sapiens" gets 4,460.
Source matches exactly "homo sapiens" gets 4,450.
Source matches exactly "homo" gets 0.
no redundantes Chains (Dunbrack, Hobohm)
|
Source* |
Sequence Identity <= |
Chains |
Resol- ution <= |
R Factor <= |
Chain length |
Non X-Ray |
Alpha Carbon Only |
|
Dunbrack |
25% |
1718 |
2.0A |
0.3 |
20-10K |
Excluded |
Excluded |
|
(7/03) |
25% |
2656 |
3.5A |
0.3 |
20-10K |
Excluded |
Excluded |
|
25% |
2666 |
3.5A |
0.5 |
20-10K |
Excluded |
Excluded |
|
|
50% |
4272 |
3.5A |
0.5 |
20-10K |
Excluded |
Excluded |
|
|
50% |
5042 |
3.5A |
0.5 |
20-10K |
Included |
Excluded |
|
|
50% |
5089 |
3.5A |
0.5 |
20-10K |
Included |
Included |
|
|
75% |
6158 |
3.5A |
0.5 |
20-10K |
Included |
Included |
|
|
100% |
38760 |
3.0A |
0.5 |
20-10K |
Included |
Included |
|
|
Hobohm |
25% |
1999 |
3.0A |
0.3 |
>30 |
Excluded? |
Excluded? |
|
(4/03) |
90% |
6254 |
" |
" |
" |
" |
" |
* Sources:
Dunbrack: http://www.fccc.edu/research/labs/dunbrack/pisces/
Hobohm: http://homepages.fh-giessen.de/~hg12640/pdbselect/
OCA: http://bioportal.weizmann.ac.il/oca-bin/ocamain
RCSB: http://www.pdb.org