Voltage gated ion channel prediction server

The aim of VGIchan server is to predict voltage gated ion channels and classify them into sodium, potassium, calcium and chloride ion channels from primary amino acid sequence using SVM method based on composition , PSI-Blast and HMM.


Supplemantary Developers

General Information and Help

General Information

Voltage-gated ion channels are integral membrane proteins that enable the passage of selected inorganic ions across cell membranes. They open and close in response to changes in transmembrane voltage, and play a key role in electric signaling by excitable cells such as neurons (Sands et al., 2005). These ion channels are important for physiological function and are critical in producing hyperexcitability. Many drugs routinely used in the clinical setting, as well as several novel experimental drugs, have shown interaction with voltage gated ion channels (Errington et al, 2005). Currently there are 1428 genome projects (http://www.genomesonline.org/ ), and out of which 263 have been published, 673 prokaryotic and 489 eukaryotic are ongoing projects. There is a need to develop in silico methods for annotation of voltage gated ion channels with high accuracy. Keeping this in mind, we compiled all the annotated ion-channels from Swiss-Prot and developed prediction method for voltage gated ion channels and further classifies them into sodium, potassium, calcium and chloride ion-channels.

Different approaches were used for prediction method like, SVM based on amino acid composition and dipeptide composition as input vector, PSI-Blast and HMM. For prediction of ion channels 82.89%, 85.56%, 84.22%, 96.22% accuracy were achieved by amino acid composition, dipeptide composition, PSI-Blast and HMM respectively. For classification of ion channels, overall accuracy of 92.88% 96.89%, 69.33%, 96.86% were achieved by amino acid composition, dipeptide composition, PSI-Blast and HMM respectively.

Stepwise HELP

Name of Protein:- This is an optional field. It can have any alphabet and numbers with "-" or "_".

Protein Sequence:-VGIchan server allows the submission of sequence in any of the standard formats. The users can paste primary sequences in the provided inbox. The server also has the facility for uploading the local sequence files.

Sequence format:- The server can accept both the formated or without formatted primary protein sequences. The users should choose whether the sequence uploaded or pasted in plain or formated before running prediction.

Selection of types of predictions:- The server allows 2 types of prediction, select them
  • Prediction of ion-channels ;
  • Classification of ion Channels;

Prediction Approach:- The server allows the prediction on the basis of four different approaches, Select any one of them
  • SVM method based on amino acid composition
  • SVM method based on dipeptide composition
  • PSI-Blast
  • HMM

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