Topology Independent Comparison of Biomolecular 3D Structures

Introduction

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The new version of CLICK web server is available at: http://cospi.iiserpune.ac.in/click

Our server is capable of superimposing the 3D structures of biomolecules, the Cartesian coordinates of whose constituent atoms are presented in the PDB format.

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 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 -

1. Proteins that are sequentially, and structurally similar
2. Proteins with multiple chains showing the feature of CLICK to align structures regardless of chain breaks
3. Proteins that are structurally similar but topologically different
4. Multi-domain proteins, where the individual domains in one structure has a structural equivalent in the other but the relative orientations between domains in the two structures is different
5. DNA double helical structures

In the new version of the server (http://cospi.iiserpune.ac.in/click), users choose between the options of pair wise alignments or database searches. 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 N. Nguyen, Parichit Sharma, Neelesh Soni, Kuan Pern Tan, Chandra Verma, and M.S. Madhusudhan.