3DTF: Transcription factor PWMs from 3D structure-based energy calculations

3DTF is a web-server to analyze the protein-DNA binding site and calculate Positional weight matrix (PWM), representing the DNA-binding specifity of the protein. More details here.

Use one of the following three options to run 3DTF (all specified inputs are required).

Task 1 mode: Submit a PDB file to be analyzed for suitability to calculate PWMs.
(For example, download and submit this file, derived from 1gcc.)

Enter the (local) filename of your protein-DNA complex 3D structure :


Task 2 mode : Submit a PDB file to automatically calculate PWMs.
(For example, download and submit this file, derived from 1gcc. Or view precalculated results here.)

Enter the (local) filename of your protein-DNA complex 3D structure :

Calculation mode: short (enough for convergence of PWM) or long (for convergence of full model)

Task 3 mode : Submit a PDB file and specify interface parameters to calculate PWMs in a user-defined way.
(For example, download and submit this file, derived from 1gcc, and specify B 3 C 24 10 as parameters.)

Enter the (local) filename of your protein-DNA complex 3D structure :

Chain ID: and base number: of starting position of the binding site on downstream (5'->3') DNA strand, ascending base number in PDB file;
Chain ID: and base number: of starting position of the binding site on upstream (3'->5') DNA strand, descending base number in PDB file;
Length of the binding site:
Calculation mode: short (enough for convergence of PWM) or long (for convergence of full model)

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Reference:
Denitsa Alamanova, Philip Stegmaier and Alexander Kel, Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies, BMC Bioinformatics 2010, 11:225
December 2011