Users can choose query structures from the PDB without having to upload their own structure files.
The input can be just the 4 letter PDB code, in which case the whole structure corresponding to that PDB entry will be considered. Should you want to specify chains and fragments use the following format:

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Format	Meaning
1ang	The whole structure 1ang.
1ang,A	The structure 1ang, chain A
1xxa,A,B	The structure 1xxa, chains A and B
1ang,A(1:15),A(82:100)	Two fragment structure constituting residues 1-15 and 82-100 of the structure 1ang, chain A.

Note: If you are uploading a PDB structure then you can not specify the fragments. If so desired, you should pre-fragment the PDB structure and then upload.

Representative atoms should be specified exactly as they appear in the PDB files (upper case, etc). The choice of representative atoms depends on the types of molecules that are to be aligned. The example of representative atoms for proteins are CA, CB, C3, N, O etc.

At the least, 3 representative atoms should be present in each of the structures to be aligned.

The user can chose one or more type of atoms as representative. For example, when aligning a pair of proteins the representative atoms chosen could be "CA CB". When choosing multiple types of representative atoms separate then with spaces.

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Structure type	Choice of representative atom(s)
protein-protein alignments	CA; Or any main-chain atom or combination of main chain atoms
DNA/RNA alignments	C3'; Or any nucleotide backbone atom
DNA-protein complexes	CA C3'; Or any combination of protein/nucleotide backbone atoms
DNA-protein complexes	CA C3'; Or any combination of protein/nucleotide backbone atoms

Note: To align ligand molecules change the HETATM label to ATOM. Choose the appropriate representative atom(s) and upload the structure.

• In addition to the cartesian coordinates of the representative atoms, CLICK can make use of other features of the protein such as secondary structure, depth, etc (see below) in guiding the alignment.

• Secondary structure provides the general three-dimensional form of local segments of proteins. For matching of a pair of cliques in our algorithm, the secondary structure score between two equivalent residues Ai and Bj are compared:

SSM[Ai,Bj]

Where,

• SSM is an empirically determined secondary structure match matrix.


• SS(Ai) is the secondary structure state of amino acid residue Ai, and s is a preset threshold for matching secondary structure elements.


• The cut-off threshold for comparing secondary structure used in this study was 2, hence SSM[Ai,Bj]< 2.


• This implies that, either residues of regular secondary structures can only match with other residues of the same secondary structure, or with residues in loops.

• Side-chain solvent accessibility is the degree to which a residue in a protein is accessible to a solvent molecule. The solvent accessibility score between two residues Ai and Bj are matched by using the inequality:

SAM[Ai,Bj]

Where,

• SAM is an empirical solvent accessibility match matrix.


• SA(Ai) is the side-chain solvent accessibility of amino acid residue Ai, and a is a preset threshold for matching solvent accessible area states.


• The cut-off threshold for solvent accessibility matching is a=1, implying that residues categorized in different accessible area classes cannot be matched.


• However, this criterion is relaxed to allow the matching of two residues in adjacent accessible area classes if their side chain accessible areas are within 10% of each other.


• Note: Secondary structure, side-chain solvent accessibility, and residue depth are currently computed only for protein structures.

The depth of an atom/residue is defined as its distance to the closest bulk solvent molecule. It is a measure that parameterizes the environment of atoms/residues. For further details on the computation and utility of Depth refer to http://cospi.iiserpune.ac.in/depth/

Currently, users can search over following structural databases:

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Serial no.	Database
1	non-redundant (90% sequence identity) set of 24,563 protein chains
2	non-redundant set of 3468 human protein chains
3	a set of 2262 DNA-protein complexes
4	non-redundant set of 493 RNA
5	non-redundant set of 1368 DNA

Uploading your own database:
The server offers the flexibility of uploading your own database, should the default ones be inadequate for your queries. The user should upload a plain/ASCII text file. The format of the file is as follows:
The first line is the type of their database (protein/DNA/RNA or DNA-protein) and next lines are just the 4 letter PDB code and/or chain - for example:

Sample file for user uploaded database

Number of hits for database search

As databases could be large, you may want to restrict the number of comparisons for which you may require detailed information (alignment files and the superimposed structures). The hits are ranked according to Z-scores.

We advise users of long running jobs to fill in this field so that they could be notified (with a link to their results) on job completion. We will neither store nor disseminate these e-mail addresses.

If no email address is provided: Please save the URL that is shown after you submit the job. You can either leave the page to refresh until completion or bookmark it to for later. Once the job finishes, result page referred by the URL will show the results.

For each alignment produced by CLICK, a Z-score is computed to determine the significance of the alignment. In our case, the Z-scores are an estimate of the likelihood that the alignment is different an alignment made by chance. It is computed as

Where,

• A is the query structure for which similar structures are sought in a database, whose members are the structures {S_i}.
• SO_A-Si is the average structure overlap (computed over the representative atoms) on the superimposition of A and S_i within cut-off distances of 1 Å, 2 Å, and 3 Å.


• avg_SO_bg and std_ SO_bg are the average and standard deviation of structure overlap within 1 Å, 2 Å, and 3 Å of alignments produced by aligning all members of a background database with one another. Background databases are chosen according to the submitted query.
• For instance, for a query protein structure, the background database would be a non-redundant set of proteins structures consisting of 1601 chains. Similarly, the DNA, RNA and DNA-protein complex databases consist of 107, 255 and 301 non-redundant structures respectively. When the query structure is a fragmented chain of a structure that consists of N representative points, the same number of points (of the same atom types) are extracted at random from 30 randomly chosen structures of the appropriate database.
• The avg_SO_bg is then computed by an all-against-all alignment of these 30 selected extracts. For the comparisons of whole molecules or for fragments containing more than 80 representative points, the background scores are computed by considering the all-against-all comparisons of structures of 30 randomly chosen whole molecules.

Note: For a significant match, Z-score should be above 2.5. The greater the Z-score the more significant is the match.