Improving a software system for protein active site determination

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2 Δεκ 2013 (πριν από 3 χρόνια και 10 μήνες)

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Improving a software system for protein active site determination

Gregory James Dodge
1
, Cyprian Corwin
2
, Herbert J Bernstein
3
,

Paul A Craig
1
.
1
Chemistry,
2
Computer Science
, Rochester

Institute of Technology, Rochester, NY,
3
Mathematics and

Computer
Science, Dowling College, Oakdale, NY

ProMol is a plugin for the molecular visualization engine PyMOL that is designed to locate the
active site on a query protein. ProMol does this by comparing the three dimensional distances of
all of the atoms in a prot
ein to the three dimensional positions of a library of known active site
residues.
This is a computationally intensive process, and it would take months to run the
entire

PDB (Protein Data Bank)

through the program
. Recently however, advances in GPGPU
(General Purpose Graphics Processing Unit) computing and GPU design have allowed simple
computations
,

such as those used by ProMol
,

to be preformed rapidly across hundreds of cores.
Utilizing GPGPU computing, the time needed to run proteins through our pro
gram could be
drastically reduced.
Due to the rapid turnover of authors on the project however, ProMol's
codebase was quite fragmented. Over the course of summer 2011, our group worked to
streamline ProMol's source in preparation for implementing GPGPU com
puting. This work
consisted of bug hunting, re
-
implementing the PDB
loading functionality, and cleaning up the
user interface, among other things.
Ideally, with these changes in place, we will be able to adapt
PyMol and Promol's selection algebra to run i
n parallel across many GPU cores.