iAlign - Structural comparison of protein-protein interfaces


Proteins usually do not act alone. From macromolecular machinery to antibody/antigen complexes, protein-protein interactions play an essential role in a living cell. How do proteins interact with each other? High resolution structures of protein-protein complexes provide valuable insights into the mechanisms of protein-protein interactions. Structural comparison of protein-protein interfaces further facilitates studies of protein-protein interaction modes and helps to infer relationship between proteins. iAlign is a program designed for the comparison of the structures of protein-protein interfaces.

Details of the program can be found in the following references:

  • Mu Gao and Jeffrey Skolnick, 2010. iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics, 26(18):2259-65. PDF and Supplementary Material.
  • Mu Gao and Jeffrey Skolnick, 2010. Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. PNAS 107(52):22517-22. PDF and Supplementary Material.

If you are looking for a tool for evaluating protein-protein docking models, check out IS-score.

This software is freely available to ALL users.

Pairwise Comparison On-line Service

Compare protein-protein interfaces of the structures of two pairs of protein complexes. All structures must be in the PDB format. Each structure must contain at least two protein chains separated by "TER". If you do not specify chain IDs, the program will perform all against all alignments of detected interfaces with at least 15 interfacial residues. Upload your structures here (fields marked with * are required):

Structure 1* Chain ID 1 ID 2

Structure 2* Chain ID 1 ID 2

Your Email Address* (a web link to iAlign results will be sent to this address)

Advanced Options

Scoring Metric TM-score IS-score
Allow Non-sequential Alignment Yes No

Download Software

You may install and run iAlign locally.

Benchmark Datasets

This page is maintained by Mu Gao. Last updated 04/01/2014.