When your request is completed, results are posted on a webpage (sample). You will be sent the link of the webpage via email. If your request is not private, your results will also be displayed in the Folding Results Database.

Each request only takes a few hours of compute time on an average desktop PC. However, depending on the request traffic, it may take a few days to process your request. You will be notified by email when your request is completed.

A folding request for a target conformation (or set of target conformations) builds a roadmap approximating the energy lanscape around the target conformation(s). Results include overall roadmap analysis as well as individual pathway analysis of transition pathways between the target conformations and representative pathways to the first target conformation.

A pathway request extracts a transition pathway between specified target conformations from an existing roadmap. Individual pathway analysis results are included on the roadmap results page.

The Secondary Structure Information File defines which secondary structure elements you want to study. You can specify secondary structure elements as ranges of residues or as sets of contacts. Residue numbers start from 1. For example, consider Protein L:

Protein L has 5 secondary structure elements (as computed by DSSP):

	beta 1:	residues 2 - 9
	beta 2:	residues 16 - 22
	alpha 1:	residues 25 - 36
	beta 3:	residues 45 - 47
	beta 4:	residues 55 - 60

The corresponding Secondary Structure Information File is as follows (comments are followed by the # sign):

	5	#total number of secondary structure elements
	RANGES	#keyword indicating the following elements are defined as residue ranges
	5	#number of ranges
	2-9	#range of residues from 2 to 9, beta 1
	16-22	#beta 2
	25-36	#alpha 1
	45-47	#beta 3
	55-60	#beta 4

You can also specify secondary structure elements as sets of contacts. For example, to specify the alpha helix as a set of contacts, the Secondary Structure Information File is as follows:

	5	#total number of secondary structure elements
	RANGES	#keyword indicating the following elements are defined as residue ranges
	4	#number of ranges
	2-9	#range of residues from 2 to 9, beta 1
	16-22	#beta 2
	45-47	#beta 3
	55-60	#beta 4
	SETS	#keyword indicating the following elements are defined as sets of contacts
	1	#number of sets

      (28 25) (29 26) (30 26) (30 27) (31 27) (31 28) (32 28) (32 29) (33 29) (33 30) (34 30) (34 31) (35 31) (35 32) (36 32) (36 33) #contact list for alpha 1

If you do not specify a Secondary Structure Information File on the submission form, it is computed automatically using DSSP.

If you specify the Secondary Structure Information File, you also need to specify a Secondary Structure Label File. A Secondary Structure Label File gives label for the secondary structure elements in your Secondary Sctructure Information File. For example, consider Protein L:

The corresponding Secondary Structure Label File is as follows (comments are followed by the # sign):

	b1	#name for beta 1
	b2	#name for beta 2
	a1	#name for alpha 1
	b3	#name for beta 3
	b4	#name for beta 4

Currently the server only handles single-chain proteins. If you submit a PDB file with multiple chains, only the first one is analyzed. We plan to add support for multiple chains in the future.

If you do not want your results available to the public, you can check the "private" box on the submission form. By selecting this, your results will not be displayed on the public results database webpage. You instead will be able to access your results through the direct link emailed to you.