Welcome to the web-portal of MS3ALIGN, the Multi-Scale Morse-Smale Molecular-Surface Aligner. MS3ALIGN is a tool to compute alignments between molecular surfaces.

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MS3ALIGN aligns a pair of surfaces in five stages.

  1. Mean curvature is computed for both surfaces.
  2. Landmark points (red spheres) on significant protrusions are located using the Morse-Smale complex of the curvature field.
  3. Correspondences between landmark points on either surface is established by comparing curvature at multiple scales.
  4. A graph is constructed where each landmark correspondence is a node. Edges exist based on pairwise geometric properties of nodes. Maximal cliques are enumerated on this graph.
  5. Each clique results in an alignment. Alignments are ranked using an approximate RMS distance between aligning portions.

Sample Result

To evaluate Ms3align, one of the experiments conducted was to study alignments of the surfaces of four ligands bound to the Dihydrofolate Reductase enzyme.
The four ligands were Folic Acid (FOL), Methotrexate (MTX), Trimethoprim (TOP), and Br-WR99210 (WRB) taken from the RCSB pdbs 1DHF, 1DF7, 1DG5, and 1DG7 respectively.
This link shows the results of this experiment.


"MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature". Nithin Shivashankar, Sonali Patil, Amrisha Bhosle, Nagasuma Chandra and Vijay Natarajan. BMC Bioinformatics, 2016, 17:26. [BMC] [VGL]


A C++ implementation of the method is available ( molshapematch-v1.1.0.tar.gz ). The code is provided under the GNU General Public License. The source code is maintained using git here . The installation, execution, and visualization instructions are available at the projects wiki page. After building, a tool named ms3align should be present in the build directory.


The tool accepts input triangle meshes in the Off format . Here, a sample execution to align two surfaces is shown. Sample surfaces are available at this location.

$ ms3align

In the above example, a text file named 2b8l_5HA_A_poc_to_2p4j_23I_A_poc.txt will be created. It contains the transformations ranked based on the quality of the alignment (from highest to lowest).
If more than two surfaces are provided then they are all aligned pairwise.
To view the help message for further instructions on modifying parameters and other options, execute the tool without any arguments.


This work was partially supported by the Department of Science and Technology , India, under Grant SR/S3/EECE/0086/2012 and the DST Center for Mathematical Biology, IISc, under Grant SR/S4/MS:799/12. Vijay Natarajan was supported by a fellowship for experienced researchers from the Alexander von Humboldt Foundation. The authors also acknowledge the support from Department of BioTechnology, India .