Advanced queries

[Instructions]

[PDB ID Form]

[Simplified Form]

[Advanced Form]

[Notes]

Instructions

You can search the MDB by using one of the following search forms. In the results you will have the option of downloading the WRL (VRML 2.0) or mini-PDB files corresponding to the sites found. You will also be able to open a new window with the MDB Java viewer and load the particular site. A link to the appropriate entry on the PDB server is also included.

Search using PDB ID(s)

Simplified Search Form

Advanced Search Form

Search for metal binding sites in which:

Metal(s): (¹)
Number of ligands: (¹)

and the metal has to have as ligands:

, AND
, AND
, AND
Nucleic acids, AND
Waters

and with a metal-ligand distance of:
Å (⁴)

And the structure containing the site:

Must have been revised or deposited in the year(s) (⁴)
With a resolution of Å (⁴)
And an r-value of (⁴)
Source of experimental data:
Author contains: (¹)

Use the dehomologized list from PDBSELECT
with at thresold of sequence similarity.
(PDBSELECT data from Sept 2001 release)

Number of results per page =
Sorted by in order

Notes:

You can enter one option or a comma separated list of options, e.g.:
1. For example for PDB IDs:
  - 1hca will search for metal sites in the protein with PDB ID of 1hca
  - 1hca,2sod,2ccp will be used when searching for the sites in the files 1hca or 2sod or 2ccp
2. Similarly, for metals:
  - zn,cu,ca,mn will search for all sites containing zn or cu or ca or mn
3. Finally, for authors, a valid query will be:
  - smith,jones,wong if you want to search for any of these authors
Only integer positive values are valid entries. Invalid entries will be forced to integers, e.g. entering "2.5" will result in the input being read as "2". Other non-numeric characters will just be converted to "0" (zero).
Positive integer values are valid entries, any other entries will result in the field(s) being ignored during searching.
A single numeric value or a range can be used in this field, e.g.:
1. For years:
  - 1998 will search for entries deposited or revised in 1998
  - 1997- will search for entries deposited from 1997 until now.
  - 1996-1998 will search for entries deposited from 1996 to 1998.
  - -1996 will search for entries deposited until 1996.
2. For other numeric values (for example resolution):
  - 2.5 will search for entries with exactly 2.5 Å resolution
  - -2.0 will search for entries with resolutions up to 2.0 Å
  - 1.5- will search for entries with resolutions of at least 1.5 Å
  - 1.8-2.3 will search for entries with resolutions in the range of 1.8 to 2.0 Å

Page maintained by Jesus M. Castagnetto (jesusmc@scripps.edu) - © The Scripps Research Institute.
Document: http://metallo.scripps.edu/advanced/index.html
Last modified: Monday, May 13, 2002 at 15:50 (PDT) - Last accessed: Saturday, May 10, 2008 at 13:35 (PDT)