Aligning Protein Structures with GR-Align (GRaphlet-based Aligner)

Noël Malod-Dognin and Nataša Pržulj

Corresponding author: Dr. N. Malod-Dognin, noel.malod@mbzuai.ac.ae

Optimal CMO alignment

GR-Align is a fast heuristic for aligning and comparing protein structures under the Contact Map Overlap maximization (CMO) paradigm. It uses a Needleman-Wunsch algorithm in which the cost of matching two residues is their graphlet degree similarity.

Version 1.5: outputs of the original software were hard to parse. Aligned residues are now labelled with their PDB IDs.

Downloads

• GR-Align 1.5 for Linux x64
• Supplementary material (PDF)

How to run GR-Align

The package contains three programs:

• CMap converts protein structures (.pdb) into contact map graphs (LEDA graphs, .gw)
• DCount computes graphlet degree signatures (.ndump) from contact maps
• GR-Align aligns protein structures (needs both contact maps and signatures)

Run any of them without parameters (or with -h) to see usage directions.

Example

Create a contact map from chain A of structure 1amk:

./CMap -i 1amk.pdb -c A -o 1amkA.gw -d 7.5

Compute its graphlet degree signature:

./DCount -i 1amkA.gw -o 1amkA.ndump

Align all structures of the Skolnick set, listed in skolnick.lst, with contact maps and signatures in ./skolnick:

./GR-Align -q skolnick.lst -r ./skolnick -o results.txt

Citation

N. Malod-Dognin and N. Pržulj. GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity. Bioinformatics 30(9), 1259–1265 (2014). https://doi.org/10.1093/bioinformatics/btu020