Welcome to HTM-ONE

Prediction of One-dimensional Structural Properties of Helical Transmembrane Proteins

Main module of this web server (HTM-ONE) takes single amino acid sequence as input and returns residue-wise prediction of several one-dimensional structural properties of helical transmembrane regions. Properties considered are: Solvent accesibility of whole residue, its side chain, main chain, polar group and non-polar group atoms, helix-helix contacting residues, and dihedral angles Kappa, Alpha, Phi and Psi.
See a sample output by clicking here
Server performance on the training data is shown here
Data set of proteins used in training is shown here

A test sequence is provided below

Copy the sequence, paste in the text box above and press the predict button to see an example of prediction using evolutionary information (PSSM).

ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGD VNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKF PNRLNLEAINYLSAGGDFKIKCVAFE

HTMONE-TEST:

HTMONE-TEST is a module of HTM-ONE, designed to estimate, how much a given structural property of a residue in TM protein differs from their expected values. Expected value is predicted using PSSM information and neural network trained on previously known structures. Predicted and observed states are compared to determine unusually structured residues. Since, helix-helix contact requires exact identification of helices, only the remaining seven (redundant) properties (viz. three ASA values, and foure torsion angles) considered for HTM-ONE are compared in this server. Users can make comparison of a structure by providing PDB code or upload a new coordiate file in the following.

Enter a pdb code

OR Select a local PDB file for upload:

Enter chain name to be considered

Reference: Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins S Ahmad, Y Singh, Y Paudel, T Mori, Y Sugita, K Mizuguchi BMC bioinformatics 11 (1), 533