JMC's Research Page

This is John-Marc Chandonia's research page. You can also visit my home page.

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My main project is the Protein Complex Analysis Project at Berkeley National Lab. I also work on ASTRAL. Until recently, I managed the data management component at the Berkeley Structural Genomics Center. I work closely with the Kim Group and Brenner Group at UC Berkeley.

I previously worked as a postdoc in the Cohen Group at UCSF, and did my graduate studies with Martin Karplus.

I am interested in several aspects of protein folding and computational structure prediction. Current projects include:

• Structural Genomics, particularly targets selection and data management/data mining.
• Computational annotation of proteomes, including prediction of protein domains from sequence.
• Evaluation of the accuracy of computational annotation methods, and improving the methods.

I have worked on the following projects:

• Threading of genomes (Drosophila, Mycoplasma genitalium) using a combination of computational methods.
• Designing a local pseudopotential based on secondary structure predictions.
• Testing the potential in sequence alignment and distant homologue recognition (threading) problems.
• Using neural networks to predict protein secondary structure and (tertiary folding) class
• Using neural nets to predict basic aspects of tertiary structure.
• Predicting correct protein backbone from lattice-fit CA coordinates.