New Technologies Developed at the BSGC
Folding Domain Prediction Program
A large fraction of full-length proteins consists of multiple fold
domains. To predict the boundaries of these fold domains for the whole
proteome of an organism, we have developed a computation method which
provides all the predicted fold domains of the organism and their
homologs in other organisms based on their similarity to known
domains in the SCOP and Pfam databases.
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BSGC LIMS System
A Laboratory Information Management System (LIMS) stores experimental
results for targets, as well as bioinformatic predictions and other
information useful to experimentalists. After investigating the
possibility of adapting a LIMS from another structural genomics center
to fit the protocols and procedures used at the BSGC, we determined
that it would be more efficient to develop a LIMS customized to the
particular experimental procedures used at the BSGC.
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Robotic Automation of High Throughput Cloning
To clone a large number of genes from genomic DNA or cDNA libraries,
and to subclone each gene into multiple expression vectors, we have
sub-divided the entire process from PCR to mini-expression screening
into 9 steps. All steps are robotized using a 96 well format.
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Optimum Solubility Screen
To increase the success rate for obtaining crystals for structural
studies, purified proteins are screened in a wide variety of
conditions (such as pH, ionic strength, and additives) to find the
solution conditions in which the proteins are soluble and homogeneous.
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On-Column Refolding
We have developed an on-column screening method for finding refolding
conditions for insoluble, sparingly soluble, or "poorly behaving"
proteins, as well as membrane proteins.
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Improved Auto-indexing of Diffraction Data
We have found that current auto-indexing programs often encounter
problems which render them impractical for use in automated data
processing applications. Therefore, we have developed improved methods
for indexing diffraction patterns from macromolecular crystals
available in the Lawrence Berkeley Lab Indexing Toolbox (LABELIT).
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Automatic Crystal Mounting and Crystal Screening
Robotic and computational processes have been developed at the
Advanced Light Source, Lawrence Berkeley National Laboratory, to
automatically screen many crystals either for their quality assessment
or for contiguous collection of multiple data sets.
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X-ray data repository
We have developed a web-based system to provide some aspects of data
management when working on many different protein targets. The system
makes use of Python, MySQL and Apache to provide a resource for
storing integrated diffraction data and running automated programs
such as HySS, SOLVE, and RESOLVE.
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Mapping Protein Fold Space
To obtain a global view of protein fold space we have developed a
computational method to map all known protein folds in a 3-D space,
where similar folds are placed close to each other and four known fold
classes are well segregated in space.
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