The Protein Coil Library: The Derived Unordered Fragment Library

Search Using a Custom List

Customized searching in the protein coil library is performed using a queue system. After filling out the form below, your job will be submitted and processed. When the calculations are complete, you will be emailed with a link to the results. Therefore, it is important to provide a valid email address with your data. After completion, results are held on the server for two weeks, when they are deleted.

PCL Custom Search Form
Please fill out the form fields below. Fields in bold are required. When you are finished, click the "submit" button, or click "clear fields" to abandon your submission and revert to the form defaults.
First Name:
Last Name:
Email Address:

Fragment Size Selection
Select the fragment sizes you wish to include in your search. The default option is to search all fragment sizes. To select multiple sizes from the list below, shift-click or control-click each entry you wish to add.

Upload List Format
Select the format of your query from one of the following list options. Currently, three lists formats are allowed.
PDB List This is a simple list of PDB ID's, with each line containing one PDB ID. Chains can be specified by appending the chain identifier to the PDB ID, e.g. 5TIMAB would query for 5TIM chains A and B, and 1HEL_ would search for the " " chain in 1HEL. PDB ID's are case insensitive, but chains are not. Finally, blank lines and lines beginning with "#" are ignored. For an example of a PDB list file, click here.
PISCES This is a list in the style of Dunbrack's PISCES culled PDB. The first four characters of each line are interpreted as a PDB ID, and the fifth character is either the chain ID or "0" for no chain. Additionally, the first line, which contains a human-readable header, is ignored. For an example of a PISCES list file, click here.
PDBSelect This is a list in the style of PDBSelect, as given by Hobohm and Sander. Lines whose first column contain an integer value, representing the identity threshold, are parsed. The second column of these lines is interpreted to be a four-character PDB ID followed by a one-character chain identifier, which is "_" for non-specified chains. For an example of a PDBSelect list file, click here.

Upload List Source
Finally, select whether you will upload your list file or whether you will cut and paste it into the space provided below.
Upload File If you wish to upload your file directly, choose the file using the button below.

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Type File Select this option of you want to cut and paste the contents of your list file, or if you want to enter the list directly. Please paste your data in to the text box below.

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