Transcript Latest developments and plans

A Molecular Replacement Pipeline
Fei Long
Chemistry Department, University of York
The site to download BALBES:
http://www.ysbl.york.ac.uk/~fei/balbes/
According to the data released on Protein Data Bank (PDB)
In 2006
Total number of protein structures solved by X-ray crystallography :
The number solved by molecular replacement (MR) :
5567
3767 (67.5%)
In 2007
Total number of protein structures released :
7332
Total number solved by X-ray crystallography :
6260 (85.4%)
The number solved by MR :
4214 (67.3% of X-ray)
.
2.4%
10.5%
MR
SAD/MAD
SIR/MIR
19.8%
67.3%
Not
Specified
Diagram showing the percentage of structures in the PDB solved by different
techniques of macromolecular crystallography in 2007
(in 10.5% of PDB entries the technique used for structure determination
is not specified clearly)
Recent Developments in BALBES:
Currently, two versions of BALBES are developed in in
parallel. Version A is the current released version in
which the internal database is continually updated and
some functions are added. Version B involves large reorganization, and is currently under test.
1. Version A ( the current released version)
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The internal database has been updated every half month. It
now contains about 16,000 non-redundant entries (out of about
50,000 PDB files) and 23, 000 domain definitions.
1. Version A ( the released version)
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The tests on newly obtained data are kept on every half month
and successful rates is between 75% and 85% (biased) each time.
It is implemented on the YSBL server. People start to use it. 140
registered users have been tried 667 time since July 2007.
It can use the user’s own database
It can use the model PDB file from a user
BALBES can be used to provide search models only
1. Version A ( the released version)
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Full test of space groups is implemented in BALBES. If a user
requests to do it, BALBES will start to find out all possible
candidates of space groups according to that in the input data
(e.g. mtz) file, and then generate a set of new mtz files. Then if
you run BALBES on a cluster, it will execute a set of jobs
simultaneously and suggest the best solution. If you run BALBES
on an individual computer, it will run all those mtz files in turn
and again suggest the best one.
Developments in BALBES:
2. Version B (based on Alexei’s blueprint)
2. Version B (larger structural reorganization)
• The complex models are more properly handled
• New algorithms to combine the different models with or without use of input
phase
• New algorithms to handle multiple domains
• New Quality factors to make decisions (testing).
2. Version B (larger structural reorganization)
• The version is currently under test (except the part using
experimental phase). Test result has showed slight better performance
than the version A.
• The problem is the presentation of the process and the results, which
currently is confusing and two complex.
The Future Developments:
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Improve the presentation of version B and release it
Sad phasing
Twins
(Not related to BALBES) I have restarted development of
a Global Optimization program, it will be tested in the next
a few weeks on JLigand.
BALBES is being used through downloading and the web server.
Several PDB files, such as 2QQ2, 2Q87, have named BALBES as
their structure determination software