This is John-Marc Chandonia's research page. You can also visit
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My main project is ENIGMA (formerly Protein Complex
Analysis Project) at Berkeley National
I also lead development of the SCOPe and ASTRAL databases, and contribute some work to KBase.
I work closely with the
Arkin Lab and
I previously worked as a postdoc in
the Cohen Group
at UCSF, and did my graduate studies with
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:
My public key for work-related communications is here: pubkey.asc.
- I previously managed the data management component of the
- Threading of genomes (Drosophila, Mycoplasma genitalium)
using a combination of computational methods.
- Designing a local pseudopotential based on secondary structure
- 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