Superimposing the 3D structures of biomolecules, the Cartesian coordinates of whose constituent atoms are presented in the PDB format. In addition to coordinates, the web server can make use of similarity of other structural features such as secondary structure, solvent accessible surface area, and residue depth to guide the alignment.

The server uses the CLICK method of first looking for cliques of points (3 to 7 residues) that are structurally similar in the pair of structures to be aligned. Using these local alignments, a one-to-one equivalence is charted between residues of the two structures being compared. A least square fit then superimposes the two structures.

CLICK is capable of aligning pairs of Proteins, Nucleic acid structures, or any other pair of molecular structures with one another. The alignments produced, identify structural similarity, even if the topology of chain connectivity is different. The method also recognizes conformational changes that may have occurred in structural domains or sub-domains in one structure with respect to the other. For this purpose, the server produces complementary alignments between the regions that have undergone a conformational change.

The user is required to upload the pair of structures to be aligned in PDB format, or to specify the 4 letter codes for structures that have already been deposited in the PDB. One or more atoms can be chosen to represent individual residues of the molecule. Residue solvent accessible surface area, secondary structure, and depth can be chosen as additional structural features to guide the alignment. In the present form these additional features are selectively fine tuned for protein 3D structural alignments.

The resulting 3D superimposition of the two structures can be viewed using the embedded JMol viewer. Below the 3D rendering of the alignment are details of the alignment such as coverage, RMSD, sequence identity, topology score, and fragment score. Help pages inform the users about how these different measures are computed. Examples of 5 different types of pair-wise alignments are listed for the information of the user -

In the new version of the server, users choose between the options of pair wise alignments or database searches. With the database search, users can mine for global or local structural similarity between their structure of interest and a database of known structures. Currently, users can search over structural databases of:

The server offers the user the flexibility of uploading their own database, should the default ones be inadequate for their queries. Another unique feature of our server is that the query structure need not be necessarily a whole structure. Fragments of structures are also acceptable as input, as long as there are 7 or more representative atoms.

To the best of our knowledge, this is the first web server that offers to align 3D structures of biomolecules, not restricted to any one type. We believe that our server will be of great help to researchers in the general area of structural biology.

Authors: Minh Ngoc Nguyen, Parichit Sharma, Neelesh Soni, Kuan Pern Tan, M.S. Madhusudhan.