PREDDIMER

Prediction tool for an ensemble of transmembrane α-helical dimer conformations

Mode 1: Predict a dimer structure
Mode 2: Analyze your dimer structure

Predict a dimer structure

PREDDIMER reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices. Predicted dimer conformations are ranked according to the scoring function (see manual for details). Below, input sequences of an interest, specify program options and launch calculations.

If you already have launched prediction and remember your unique task ID, go to the results page.

Modeling sequences

Choose the mode of modeling:

Homodimer Heterodimer

Chosing “Homodimer” assumes identical sequences for both helices

Sequence

Length should be 20–35 residues

Name

Sequence 2

Length should be 20–35 residues

Name 2

Options

Antiparallel dimer: check if you want the second helix be rotated “upside down” Make maps: draw cylindrical maps of hydrophobic properties for each helix in dimer

pH value is used to assume protonation states of ionizable residues

If e-mail addrress is specified, you will receive a message with a link to your results

If you know ID of your task, you may go to the Results page

Build cylindrical maps of your dimer structure

In this mode you may upload your own structure of two interacting α-helices to build a cylindrical map of hydrophobic properties and mark an interface on the map. You have to choose two separate PDB files (one for each helix) and upload them to the server.

You are responsible that both PDB contain α-helices and these helices interact each other.

Choose two PDB files

PDB 1

PDB file with first helix

Name 1

This is optional

PDB 2

PDB file with second helix