VAST Search: Frequently Asked Questions
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VAST Search is a World Wide Web service for an "on the fly" search for 3D structural neighbors of a query protein. A search is initiated by submitting files of the coordinates interactively to the VAST search World Wide Web site. If you have refined the structure of the query protein using the program X-PLOR, you are required to submit an X-PLOR PSF or protein structure file in addition to the coordinate file.
What is X-PLOR and why is there a separate button for X-PLOR PDB files?
X-PLOR is a program for determining and refining three-dimensional structures of proteins and nucleic acids by X-ray crystallography and Nuclear Magnetic Resonance spectroscopy (NMR). Currently, about 80% of new structures submitted to the Protein Data Bank have been solved using X-PLOR. Therefore, 80% of the potential users of VAST Search will submit to the service with XPLOR generated files. Because of differences in syntax and nomenclature between X-PLOR PDB files and Brookhaven PDB files, X-PLOR is provided as a separate option in the service. If you have used other software packages to solve your structures, i.e., PROLSQ, TNT or MSI DISCOVER, coordinates for these structures will be accepted only if the PDB files of these structures conform to Brookhaven formats. Click here to read the Brookhaven PDB contents documentation.
What is a Biostruc and what does it mean when the error message "Missing Biostruc" appears?
Biostruc is a file format specificed in data description language called ASN.1. It includes a complete chemical description of a molecules, which is not present in PDB formatted files. Biostruc format allows the submitter to view the structure of the query protein and alignment superpositions with it's neighbors in Cn3D and is needed to browse the list of neighbors. When the error message "Missing Biostruc" is returned, the means that this file was not created and the search for neighbors cannot begin.
How long do I have to wait for the launch page to appear after pressing the Submit Request button?
The amount of time needed for the server program to send back the launch page depends on the size of the query protein, the number of chains the protein, and the CPU load during the submission process. A protein composed of a single chain and about 100 amino acids will almost always take less than a minute. An immunoglobulin with two chains will take somewhere between minute and a half to two minutes. Since VAST search calculates structure neighbors of each individual chain, we strongly recommend that you submit a separate job for each chain.
How can I save the alignments?
Search results will remain on the server for a week to allow you time to save the hit lists and the alignments. The HTML page containing the list of neighbors can be saved locally and reloaded into your browser. Alignments can be saved in either binary or text ASN.1 format to be viewed locally with Cn3D. For any hit list of five or more neighbors, a maximum of five neighbors can be viewed with Cn3D and saved in ASN.1. Alternatively, you can save the alignments of the query protein and a single hit as a kinemage file to read with the program MAGE or save the rotated PDB file of each neighbor, which should allow you to view the alignments with a program that reads PDB files.
Do I need Cn3D to examine the list of structure neighbors?
No. You have the option to view the alignments with any graphics program of your choice, but we recommend you view the structural alignments with Cn3D, which we distribute for free with VAST Search.