CLIP--Sequence Co-evolutionary Information Based Linear Interacting Peptides

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The server is designed for the prediction of linear interacting peptides from protein sequences using co-evolutionary information. The server generates binary annotation and numeric score for each residue in the input protein sequence. Larger values of propensity denote higher likelihood to bind.

Help

The webserver accepts either single or multiple protein sequence(s). The input is limited to 3 protein sequences. The user should submit the protein sequence(s) in the FASTA format.

The format of the input file is as follows:

• Line1: >protein ID
• Line2: protein sequence (1-letter amino acid encoding)

Each protein requires two lines and multiple proteins should be placed in consecutive lines.

Here is an example input file.

Materials

Datasets

• Training dataset (TR1000): Click here to download
• Test dataset (TE440): Click here to download
• Test dataset (TE275) containing shorter than 750 amino acids proteins from TE440: Click here to download
• Independent test dataset from MoRFChibi (EXP25): Click here to download

The format of the datasets is as follows:

• Line1: >protein ID
• Line2: protein sequence (1-letter amino acid encoding)
• Line3: annotation of LIPs (1 - LIPs; 0 - non-LIPs)

References

Upon the usage the users are requested to use the following citation:

• Peng Z, Li, Z, Meng Q, ZHAO B, Kurgan L, 2022. CLIP: Accurate Prediction of Disordered Linear Interacting Peptides from Protein Sequences Using Co-evolutionary Information. Briefings in Bioinformatics, 24(1):bbac502

Acknowledgments

We acknowledge with thanks the following software used as a part of this server:

• DISOPRED3 - Prediction for disordered regions
• HHBlits - Algorithm for homology detection by iterative HMM-HMM comparison