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SAP-DB: the database of Structurally Ambivalent Peptides

1. Description
SAP-DB is a Web-based database application for finding the structurally ambivalent peptides for an input protein sequence.
The purpose of this online system is to characterize structurally ambivalent fragments in proteins. The database consists of all SAPs of length 5 or greater which exist in two different backbone conformations. The data is searched and retrieved from Protein Data Bank achieved through a technique discussed in the paper by Igor B. Kuznetsov and S. Rackovsky.Sequence fragment that exists in two dissimilar conformations in two different proteins is referred to as SAP. SAP-DB System also allows users to search for SAPs based on different input criteria such as PDBID and Secondary Structure.

2. Upload input protein sequence
Input protein sequence can have upper case, lower case or mix of both upper and lower case characters. The result is always displayed in upper Case. Users need to browse and select the input protein sequence in FASTA format.

FASTA sequence file format: A FASTA file consists of a header line that begins with ">" character, followed by an optional sequence name and then the whole sequence. Input sequence works even without header information which starts with symbol ">".

Sequence string: Sequence string should be represented using the one-letter amino acid codes, which includes twenty characters for twenty amino acid types:
A - Alanine M - Methionine
C - Cysteine N - Asparagine
D - Aspartate P - Proline
E - Glutamate Q - Glutamine
F - Phenylalanine R - Arginine
G - Glycine S - Serine
H - Histidine T - Threonine
I - Isoleucine V - Valine
K - Lysine W - Tryptophan
L - Leucine Y - Tyrosine
And the following three characters:
B - Aspartate or Asparagine
Z - Glutamate or Glutamine
X - Unknown

Figure 1.1

Upon clicking the Submit button, SAP-DB system searches and displays the results containing Structurally Ambivalent Peptides as shown below.

Figure 1.2

Additional information for SAPs: User can get the additional information about the SAPs by clicking on the hyperlinks.

Figure 1.3

[Definition of the terms] Figure 1.4


3. Paste input sequence
Paste the input protein sequence into the text field to get the SAPs and its additional information.
The input sequence has to be in the FASTA format.

Figure 1.5

SAP-DB system searches and displays the results containing Structurally Ambivalent Peptides as shown in Figure 1.2.
Additional information for SAPs refer Figure 1.3 and Figure 1.4.

4. Search SAPs by Secondary Structure
Enter the secondary structure input, which are combination of DSSP Code from {G, H, I, T, E, B, S and C}
G = 3-turn helix . Min length 3 residues.
H = 4-turn helix . Min length 4 residues.
I = 5-turn helix . Min length 5 residues.
T = hydrogen bonded turn (3, 4 or 5 turn)
E = extended strand in parallel and/or anti-parallel beta-sheet conformation. Min length 2 residues.
B = residue in isolated beta-bridge (single pair beta-sheet hydrogen bond formation)
S = bend (the only non-hydrogen-bond based assignment)
Amino acid residues which are not in any of the above conformations are assigned as the eighth type 'Coil': often codified as C (coil).
If you want to search by multiple secondary Structures,enter input in comma separated format. Comma denotes the "and" operator.

Figure 1.6

Figure 1.7

Additional information about SAPs Refer Figure 1.3 and Figure 1.4.

5. Search SAPs by PDBID
User is able to search Structurally Ambivalent Peptides by entering single PDBID of 4-5 character long.

Figure 1.8

Figure 1.9

Additional information about SAPs Refer Figure 1.3 and Figure 1.4.

6. References and Citation
If you use this database application please cite the following:
On the properties and sequence context of structurally ambivalent fragments in proteins
Igor B. Kuznetsov and S. Rackovsky
Protein Science (2003), 12:2420-2433

The application works in Mozilla Firefox, Internet Explorer, Google Chrome and Chrome Plus.