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.

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] < s

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]< a < s

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.
• Depth measures the closest distance of a residue/atom to bulk solvent. A detailed description of the computation of depth can be found here.

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://mspc.bii.a-star.edu.sg/depth/

Heurisitics are applied to ensure local chain connectivity.Chain connectivity is broken when equivalent residues are not contiguous in sequence ( eg. residue highlighted in the figure below).

The equivalent residue matches before the application of heuristics is shown in the output file linked to "Matched residue pairs".

Rules:

Matched segments must have a minimum length of 5 residues (gap matching not included). Residue matches that do not follow this criteria are removed.

Adjacent segments separated by 5 or less residues are joined together.