information here
Dismiss

Computation of transfer free energies (TFEs) of transmembrane beta-barrel proteins (TMBs)

The TMB-TFE server compute transfer free energies (TFE) of amino acid side chains of a transmembrane beta berrel protein (TMB). For a beta barrel protein of interest, the transfer free energies of side-chains of all 20 amino acids in a given host position are computed respectively, and the values are reported with respect to alanine. The computation can be done using either just the sequence infomation or the structural information.
Please select the pdb file to be uploaded and specify the SeqID of the residue of interest
Only the pdb file generated by the OPM server is supported so far.
This service does not support barrel proteins formed by multichains (eg. α-hemolysin). For TFE computation of this kind of TMBs, please contact Wei Tian (wtian7@uic.edu).



Please enter the sequence of the TMB and the seq id of the residue of interest below
Any format annotation (eg. fasta header) shall be removed. Each strand shall be labeled with ">" and "<", and the residue on the midplane shall be labeled with "|" and "|".
For example, "...KDNT>WYTG|A|KLGW<SQY...." is a properly labeled sequence of a strand, where ">" marks the start of the strand, "<" the end of the strand, and residue between the two "|" (A in this case) is the one on the midplane.
The OPM server is recommended to determine the position of midplane. Alternatively, you may make a guess of its position, since our algorithm does not require an accurate position of midplane. But be aware the results in this case might not be as accurate.
Please note that the seq id is the number of the residue of interest in the sequence entered below, not necessarily the same as the one in a pdb file.
Example input of OmpLA 210



Please enter the id of the job you submitted

If you use the TMB-TFE server in your work, please cite the following paper:
Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins.
Wei Tian, Meishan Lin, Hammad Naveed, Jie Liang. 2017, Bioinformatics.
DOI: 10.1093/bioinformatics/btx053

If you have any question, please contact Wei Tian (wtian7@uic.edu).