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Folding Submission Form


Fields marked with a red asterisk (*) are required.


User Information


Full Name*: Display Name:
Email*: Affiliation*:
Position*: Advisor (if a student):



Submission Parameters


Protein Description
Protein Name*:
 
Enter the Databank Name or Submit your own file(s) *:
*** Restriction *** Multiple files must have the same amino acid sequence. *** Restriction ***
PDB Name: or Submit own File:
Native State or
Conformation #2 or
Conformation #3 or
Conformation #4 or
Conformation #5 or
 

Secondary Structure (optional)
computed automatically if not specified,
see FAQ for more details
Information File:
Label File:
 

Processing Options
Would you like your submission kept private?
Would like to create a movie of the dominant path?


Comments and Notes
(e.g., You would like all the sampled conformations, or you
would like us to generate a particular number of samples, you
would like us to generate more/fewer samples near one of the
user provided conformations, you would like to credit this protein
to someone, or you would like to put a citation to your work, etc.)


Output Samples

The roadmap is an approximation of the protein's energy landscape that consists of thousands of representative pathways to (and between) the above target conformation(s). Below we provide Roadmap Analysis and Individual Pathway Analysis.


Roadmap Analysis

Results providing global information about the entire roadmap including Ramachandran and potential energy vs RMSD (to the first target conformation) plots of all conformations in the roadmap and a secondary structure formation order (SSFO) classification of all the pathways in the roadmap (to the first target conformation).


Ramachandran Plot Potential-RMSD Plot Rigidity Map Plot: Target 0 Cluster Map Plot: Target 0 SSFO Classification of Pathways (Rigidity)
Population Kinetics Plot Helix Formation Tryptophan Contact Formation Relative Exchange Rates

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Individual Pathway Analysis

Results providing information about individual pathways are presented for two types of pathways: pathways between pairs of target conformations and a representative pathway for each secondary structure formation order (SSFO) found in the roadmap. For each pathway, we provide information about the start & final conformations, profiles of the potential energy and the number of native contacts of the intermediate conformations along the pathway, a timed contact map for the pathway, and animations of the pathway.


Pathway Name Start Final Energy Profile DOF Profile RMSD Profile Relative RMSD Profile Rigidity Distance Relative Rigidity Distance Cluster Distance Relative Cluster Distance Contact Profile: all Contact Profile: hydro Contact Map: all Contact Map: hydro Animation Rigidity Map Animation Cluster Map Animation
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We will email you when your submission is ready. Normally submissions take a few days to process.

If you have any questions or comments, please email proteinfolding@cs.tamu.edu.



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