Protein Structure Prediction using Neural Networks

Presently, I am coding a neural network for protein secondary structure prediction. Initially, I thought of predicting contact maps. But, the I coudn’t find contact map data for proteins. Moreover, parsing the PDB files and then creating a contact map seemed as a daunting task to me.

Therefore, I chose the secondary structure prediction. Well, what I am gonna do is to input a amino acid sequence and then predict secondary structure for each residue. Current methods achieve around 75-80% accuracy, so I will try to achieve atleast 75% accuracy.

My process will be a 3 stage process. First two will involve a neural network and the third one assigns confidence to prediction based on statistical information.

Any ideas, comments or suggestions?


This entry was posted on February 10th, 2006 and is filed under Biology, Technology. You can follow any responses to this entry through the RSS 2.0 feed. You can skip to the end and leave a response. Pinging is currently not allowed.

 
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No Responses to “Protein Structure Prediction using Neural Networks”

  1. Anonymous
    20. February 2006 at 08:43

    Hey,
    I am currently looking into several machine learning techniques for protein structure prediction. I have coded the program in Python and am training it. But, the problem is that Python is really really slow.

    I have 220 inputs and around 18000 samples (testing and training).. It just crawls under this..

    However, for other ML techniques, I plan to use ready-to-use software such as Weka or Yale.. Another option is using Orange library for Python.. But again, Python is damn slow.

    My inspiration: Well, when I checked on the internet about currently used ANNs for prediction, I was fascinated by their real world applications.. I wondered if these black-boxes can really learn anything about protein structure.. Hence, I tried to code a neural network for myself..

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