DANGLE

DANGLE: Dihedral ANgles from Global Likelihood Estimate

File Formats

Input: Chemical shift file
Output: Prediction table, GLE diagrams and CNS .tbl file

Input file

DANGLE takes only one input file, which contains the primary sequence and the chemical shift table.

Download a sample file

All information should be put in-between a pair of tags:

<seq_1>...</seq_1>	Mandatory	The primary sequence of the query protein in single letter code; can contain white spaces, be in lower or upper case, or use "X" to represent unknown residues.
<res_0>...</res_0>	Mandatory	The residue number of the first amino acid in the primary sequence given in the "seq_1" fields; must be ≥ 0.
<cs_data>...</cs_data>	Optional	Chemical shift data for the query protein; each line should contain the residue, residue code, atom_name and chemical shift value. Residue code can be in 3- or 1-letter-code. Chemical shift values are expected to be properly referenced.
<-!...->	Optional	Comment field; not read by the program.

You can add other information for book-keeping purposes, DANGLE does not read it.

Output files

1. Prediction Table (danglePred.txt)

This file contains all the prediction information in columns: num of islands in GLE diagram, φ and ψ predictions, upper and lower limits, and secondary structure assignments.

2. Global Likelihood Estimate Diagram (Res_X.pgm)

Each residue has its own GLE diagram, unless it has been rejected (i.e. having more than a user-defined number of islands). The GLE diagram is created in the black-and-white PGM format. It can be converted to a coloured PGM diagram with a given script or other software.

PGM	PPM

3. Dihedral Constraints in CNS .tbl Format (danglePred.tbl)

This .tbl file defines the φ and ψ constraints predicted by DANGLE and can be used directly in the ARIA program for structure calculation.

Last updated 22 Jan 2010 by Nicole Cheung.