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FTDyn is a server designed for hot spots analysis on structural protein ensembles, using the computational solvent mapping method implemented in FTMap. FT is for "Fast Fourier Transformation", which the sampling method is based on, and Dyn is for Dynamic. FTDyn takes as input an ensemble of structures in the format of a MODEL/ENDMDL divided PDB file, then prepares and submits an individual job for each structure to FTMap using a faster protocol. The mapping results are provided in the format of frequencies of probe-residue interactions.
Input
The interface for submitting jobs is shown below. If you are using a structure from the PDB, you should specify the PDB id and chains, otherwise, you may upload your own PDB file. Note that any HETATM records are stripped out, removing any ligands in the file. Below, the user has decided to map the PDB id 1z1m, which includes 24 structures of MDM2 obtained from NMR.
Once you correctly fill in the form and hit the 'Map Ensemble' button, you will see a success message as below. When the job is complete, you will receive an e-mail with a link to the results.
Output
FTDyn analyzes results from FTMap by calculating the number of nonbonded and hydrogen bond interactions between all solvent probes and each residue using HBPlus. These interactions are calculated for each structure in the ensemble.The format of these files is
Residue_Number Chain Residue_Name Percent_Contacts
As an example, this shows that 12.929% of all probe-protein interactions involve Leucine 54 on chain A of the protein
54 A LEU 12.929
These interactions are also written into column 61-66 of a PDB file of submitted structures for users to download. Since these columns represent temperature factors, some molecular viewers can be used to visualize the result by coloring the residues based on these numbers. For example, in PyMol, one can do it using this command, after rec.nonbonded.pdb is loaded.
PyMOL> spectrum b, blue_red, rec.nonbonded
Once an individual job is complete, the interactions can be dynamically plotted on the job results page by clicking View link in the Fingerprint column. When mapping of all structures finishes, an averaged fingerprint is calculated and can be plotted by clicking the Fingerprint link after Average.
The mapping results are also shown on the results page using JSmol. By default, the residues are colored on a spectrum from blue to red, indicating the frequency of probe interactions from zero to maximum. User can also color the protein by direction or secondary structures using the radio buttons. A command line box is provided so one can execute arbitrary Jmol commands to control the view.
Combined results: after all structures are complete, the individual interactions are combined, and can be downloaded in different formats:
.pdb: one PDB file including all submitted models divided by MODEL/ENDMDL, with the interactions written in columns 61-66.
.pse: PyMOL session containing all the structures with residues colored from blue to red based on contact frequency.
.tar.xz: an archived directory containing all the mentioned individual contact files, pdb files, and combined files.
In Windows, 7-Zip can be used to open the file. To extract this file in bash, do, e.g.
$ tar xvfJ 424b991f-9546-4fef-a662-2f4f00116925.tar.xz
average.hbond.txt, average.nonbonded.txt: averaged interactions of all structures' mapping fingerprints. Note that this calculation assumes the structures submitted have the same residues.
FAQ
My job failed. What does this mean?
A failed job could have one of the following statuses.
Unknown Chain or Residue:
First, check whether your input is in standard PDB format, with multiple
structures divided by MODEL/ENDMDL. The server only supports the 20 standard
amino acids. Any non-standard atoms should be removed from the pdb file
before submitting the server.
Protein too large for FTMap:
If your protein is huge (>>1000 residues), our computers could run out
of memory. In this case, it is suggested to submit a smaller unit of the
protein to the server, e.g. one domain of a multi-domain protein.
If you are still unsure, please use our contact form to ask about your job.
My question isn't answered here, how can I reach you?
Please use the contact form on our lab website