|
 |
Faculty and Student
Teams Program
|
Project Descriptions
Lawrence
Berkeley National Laboratory
Chemical Bonding Parameterization
Requesting applications from science or engineering faculty members
at institutions serving students underrepresented in science, engineering,
mathematics and technology, to work at LBNL.
Project Description
Macromolecular crystallography requires the computational optimization
of the atomic model with respect to the experimental data. To minimize
over-fitting of the diffraction data, this optimization process includes
restraints derived from a priori chemical information, such as bond lengths
between covalently connected atoms. The parameterization of these chemical
interactions is a critical component of the optimization procedure1. Currently,
several parameterization sets exist for protein molecules and nucleic acids.
It is often a time consuming process to establish the correct model parameterization
prior to refinement. This is particularly true when novel ligands, such
as drug candidates are being studied. The need for greatly increased throughput
of protein structure determination requires increased reliability and automated
assignment in the parameter sets. The goal of the project is firstly to
create a state of the art set of model parameters for crystallographic
refinement, based on the currently available chemical information. Secondly,
methods to automatically assign parameters to novel small molecules will
be investigated.
1Engh, R.A. and Huber, R. (1991). Accurate Bond and Angle Parameters
for X-ray Protein-Structure Refinement, Acta Cryst. A47, 392-400.
Applicants Responsibilities and Relationship to Project
Applicants and their students will receive
support under the Department of Energy Faculty and Student Team (FaST)
program to work collaboratively
with a research group at Berkeley Lab for 10 weeks during the summer of
2008. Faculty and students
team members will be assigned to the same research group and typically
faculty participants will provide mentorship and/or advising support to
the undergraduate student team members while at the Lab.
Applicants are encouraged to contact Berkeley Lab investigators
offering FaST opportunities during the application process.
Following the summer appointment, it is anticipated that the
faculty participants will establish a ongoing collaborative relationship
with Berkeley Lab investigators and assist in recruiting undergraduate
students from their campus for DOE internship programs.
Qualifications of Ideal Candidate
| Faculty: |
Ph.D. in chemistry, biochemistry, biology or related fields. Experience
with computers and computer programming would be very advantageous.
Works well in a collaborative environment with students. Collaborates
with students in his/her field. Willing to work at LBNL for an extended
period (2-3 summer months, or longer). |
| Student: |
Working towards an AA or BS in Chemistry, Biochemistry, with an
interest in computation. Must work well in a highly collaborative
research environment with faculty, senior researchers and other students.
Willing to work at LBNL for an extended period. |
Support
and Financial Commitments
See Financial
Information.
For More Information Contact:
Laurel
Egenberger
Manager
College
& University Programs
Lawrence
Berkeley
National Laboratory
E-mail: LLEgenberger@lbl.gov
Phone: 510-486-5190
|
Dr. Paul Adams
Physical Biosciences Division
E-mail: PDAdams@lbl.gov
Phone: (510) 486-4225 |
|
