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 ENIGMA (formerly Protein Complex Analysis Project) at Berkeley National Lab.
I also lead development of the SCOPe and ASTRAL databases, and contribute some work to KBase.

I work closely with the Arkin Lab and Brenner Lab 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 interests include:

• Analysis of genome-scale networks (e.g., protein interaction, metabolic, and regulatory). How can they be accurately defined based on experimental data, how do they relate to one another, and how do they evolve?
• Protein-protein interaction data, and the evolution of stable protein complexes.
• Computational annotation of proteomes, including prediction of protein domains from sequence, and homology prediction.
• Structural Genomics, particularly target selection strategy.
• Evaluation of the accuracy of computational annotation methods, and improving the methods.

I have worked on the following projects:

• I previously managed the data management component of the Berkeley Structural Genomics Center.
• 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 homolog 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.