Help

Text Search

The text search page allows you to search single fields and multiple fields in combination.

• The text search page allows you to search single fields and multiple fields in combination.
• Find the content of the field you want to search in the collapse menu of different types (Protein Information; Peptide Basic Information; Peptide Physicochemical; Affinity Information; Literature).
• Enter or select the single field or multiple field combination you are interested in in the corresponding area.
• Click"Submit"(or click "Reset" to clear your input).

Structure Search

The text search page allows you to search single fields and multiple fields in combination.

• The Structure search page allows you to search single fields and multiple fields in combination.
• Find the content of the field you want to search in the collapse menu of different types (PDB ID; Method; Peptide Length Range; Residue Modification; Release Year Range ).
• Enter or select the single field or multiple field combination you are interested in in the corresponding area.
• Click"Submit"(or click "Reset" to clear your input).

Foldseek Search

The Foldseek search page allows you to enter a Sequence or upload a file (PDB/CIF format) to perform retrieval and comparison analysis of PPIKB

• Select the corresponding program (Foldseek easy-search or Foldseek multimer-search).
• Enter the sequence or upload the file (PDB/CIF format).
• Select Mode (3Di/AA or TM-align) and Format mode (BLAST-TAB or Pretty H).
• Click"Search"(or click "Reset" to clear your input).

Note:

• Inputting amino acid sequences only supports 3Di/AA+BLAST TAB.
• Foldseek multimer-search program only supports structure input.

BLAST Search

The BLAST (Basic Local Alignment Search Tool) program uses a strategy based on matching sequence fragments by employing a powerful statistical model to find the best local alignments (For more information see http://www.ebi.ac.uk/Tools/sss/ncbiblast/).

Usage Introduction

Step 1 – Sequence Input

• Sequence Input Window: The query sequence can be entered directly into text area. The sequence must be FASTA format.

FASTA format: FASTA formatted sequence records start with a definition line, which must start with a > character. The definition line must occupy one single line and followed by sequence data.

Example:

>
FLPLLAGLAANFLPTIICKISYKC

Step 2 – Parameters

• Matrix: This option allows you to choose the scoring matrix to be applied to the search.

Default value is: BLOSUM62

Tip: In general, higher value BLOSUM matrices (e.g. BLOSUM90) and lower value PAM matrices (e.g. PAM30) are more stringent than low value BLOSUM or high value PAM matrices. This implies that if you want to find more distantly related homologues, you should preferentially employ a low value BLOSUM or high value PAM matrix (For more information about scoring matrices see http://en.wikipedia.org/wiki/Matrix).

SMILES Similarity

This tool is used to perform retrieval analysis on PPIKB based on SMILES Similarity, and different algorithms can be selected.

Algorithm selection: tanimoto; dice; cosine; kulczynski.

Number of output results: 5; 10; 100; all.