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Paul Adams, Component Project Leader

BSGC Role

Dr. Adams is a crystallographic software developer and structural biologist. He will oversee the design and implementation of the new PHENIX software for high-throughput crystallography, and lead the effort to automate diffraction data processing and structure determination. He also serves as the Deputy of the overall project and will help coordinate the activities of the various groups.

Component Project Information

Our role is to provide the computational support needed for rapid structure determination. This support, by necessity, will be organized into two parallel strategies. For the short-term support, pre-existing software systems will be maintained and integrated with one another as far as is possible. Concurrent with this a new software system, called PHENIX, will be designed and built. In the long-term, this new integrated system will be provided to the participants of the Structural Genomics Center as their main tool for rapid structure determination.

Short-term support
A scientist will be responsible for interacting with the other members of the Center who are involved in solving structures. He or she will provide expert knowledge and streamlined software, which will enable the rapid solution of structures. He or she will be required to maintain existing software packages and develop ways for these programs to be integrated into user-friendly tools for others to use.

Long-term support
In collaboration with other researchers (T. Ioerger, R. Read, J. Sacchettini, and T. Terwilliger) a new software system is being constructed for the rapid, automated determination of structures by X-ray crystallography. This PHENIX system is built on a strong foundation that can accommodate current plans and future developments. A toolkit will be developed to provide an environment for integrating the implementation of crystallographic tasks and automated decision-making. The framework for the toolkit is the Python system, which provides a powerful object-oriented scripting language. A fundamental feature of the toolkit is that the entire history of the structure solution, along with all the structural information generated, will be stored in an object-oriented database. The PHENIX system will permit all tasks required for the computation of phases, automated map interpretation, model building and refinement, to be integrated with newly developed procedures for automated decision-making. Our ultimate goal is the development of a system that will take X-ray diffraction data and rapidly produce minimally biased atomic coordinates with little or no human intervention.

     
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