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Research: Human Proteome Folding - Phase 2: Research Participants
Research Participants

New York University:

Dr. Richard Bonneau:  Dr. Bonneau is the technical lead on the Human Proteome Folding project. Dr. Bonneau has expertise primarily in ab initio protein structure prediction, protein folding, and regulatory network inference. He is currently focused on applying structure prediction and structural information to functional annotation and the modeling/prediction of regulatory and physical networks. Dr. Bonneau working to develop general methods to solve protein structures and protein complexes with small sets of distance constraints derived from chemical cross-linking. At NYU Dr. Bonneau also works on a number of systems biology data-integration and analysis algorithms, including algorithms designed to infer global regulatory networks from systems–biology data.

Kevin Drew, Research Assistant:  Kevin is the Lead Software Engineer on the HPF project. He is mainly interested in predicting function from ab initio structure predictions. Specifically he is interested in predicting structure and function for new protein families. He has worked in the past on grid solutions to analyzing mass spectrometry data for proteomics research. Kevin handles the development of function prediction algorithms from HPF data and the pre and post processing of HPF data.

University of Washington:

Dr. David Baker:  Rosetta was developed initially in the laboratory of David Baker by a team that included a large number of scientists (now at several institutions). The goal of current research in his laboratory is to develop improved models of intra and intermolecular interactions and to apply improved models to the prediction and design of macromolecular structures and interactions. Prediction and design applications can be of great biological interest in their own right, and also provide very stringent and objective tests which drive the improvement of the model and increases in fundamental understanding. More

Lars Malmstroem:  Lars Malmstroem has worked to engineer the infrastructure (at the ISB/UW end) needed to handle the vast highly interconnected data–sets that this project will generate; he will also be heavily involved in developing the correct data–integration schemes to best deliver the resultant predictions to biologists.


Bonneau lab: http://www.cs.nyu.edu/~bonneau/R.Bonneau-lab.html
David Baker: http://depts.washington.edu/biowww/faculty/baker.html
Rosetta commons: http://www.rosettacommons.org/


Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. (2004) Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.Genome Biology. 5(8):R52-68

Bonneau, R & Baker, D. (2001). Ab Initio Protein Structure Prediction: Progress and Prospects. Annu. Rev. Biophys. Biomol. Struct. 30, 173-89. Review.

Rohl C, et. al. Protein structure prediction using Rosetta. Methods Enzymol. 2004;383:66-93.


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