This server is designed for the prediction of calcium binding residues. It produces both binary value (a residue is predicted as calcium binding residue or non calcium binding residue) and numeric socre (the putative propensity of a residue binds to calcium) for each residue in the query proteins.

Please follow the three steps below to perform a prediction

STEP ONE   Paste no more than FIVE protein sequences with standard FASTA format:

  To make a blance among various predictors that deployed on this server, we limit the computation resource for SCAMPER. For large-scale predictions, you are welcome to send your protein sequences to us via jianzhang@xynu.edu.cn or biocomputinglab@sina.com

  Click Here to Use Example Protein Sequence

STEP TWO   Set a judgement threshold:

  Recommended threshold 0.612 (specificity=90%)

STEP THREE   Provide you email address:

  The prediction results will be sent to your mail box

HELP

SCAMPER can accept five protein sequences for a single prediction. Please contact biocomputinglab@sina.com for large-scale prediction quest. The users should input the protein sequences in standard FASTA format, which begins with a symbol ">". The format of the input protein sequence is as follows:

    Line 1: > PDB ID or UniProtKB ID or any other annotation(s)

    Line 2: protein sequence (1-letter amino acid encoding)

The judgement threshold that input in STEP TWO  will be used to generate putative calcium-binding annotations.

We send a message to your email address once the your job is finished.

Materials

TRAINING dataset Download

TEST dataset Download

The format of the above files is explained here.

Putative calcium-binding proteins in human proteome Download

Acknowledgments

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

UniProtKB- UniProt Knowledgebase

IUPred2A- Prediction of Intrinsically Unstructured Proteins

ASAquick- Fast neural network-based predictor of solvent accessibility

HHBlits- Algorithm for homology detection by iterative HMM-HMM comparison

PSIPRED- Prediction of secondary structure