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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