PDB ID: 2G2U
SHV-1 Beta-lactamase, in complex with
Beta-lactamase Inhibitor Protein (BLIP)
PDB ID: 2G2W
SHV Beta-lactamase, D104K point mutant
in complex with Beta-lactamase Inhibitor Protein (BLIP) |
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Research Interests:
Development and use of software for
modeling protein/small molecule and protein/protein interactions.
Design and engineering of protein interfaces. Development of software
for computational protein design and visualization/evaluation of
protein energetics. Experimental characterization of protein complexes
via crystallography and mutagenesis. Communicating science through computational tools
and writing.
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Publications:
K.A. Reynolds , M.S.Hanes, J.M. Thomson,
A.J.Antczak, J.M. berger, R.A. Bonomo, J.F. Kirsch and
T.M. Handel. "Computational Redesign of the SHV-1
Beta-lactamase/ Beta-lactamase Inhibitor Protein
Interface." Manuscript accepted (2008). Work from
this paper was presented by Dr. Handel at the 21st
symposium of the Protein Society (2007) and highlighted in
Vol. 85 of Chemistry and Engineering News.
A. Chowdry, K.A. Reynolds, M.S.
Hanes, M.S. Voorhies, N. Pokala, and T.M. Handel. "An object-oriented
library for computational protein design." Journal of Computational
Chemistry, 28(2007): 26745-26753.
K.A. Reynolds, J.M Thomson, K.D. Corbett, C.R.
Bethel, J.M. Berger, J.F. Kirsch, R.A. Bonomo, and T.M. Handel.
"Structural and computational characterization of the SHV-1
Beta-lactamase/Beta-lactamase Inhibitor Protein (BLIP) interface."
Journal of Biological Chemistry, 281(2006): 26745-26753.
S. M. Godzina, M. A. Lovato, M. M. Meyer, K. A. Foster, W. K.
Wilson, W. Gu, E. L. de Hostos, and S. P. T. Matsuda. "Cloning and
characterization of the Dictyostelium discoideum cycloartenol synthase
cDNA." Lipids, 36 (2000): 249-255.
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| CV: [html]
[pdf] |
Open-source software projects:
The EGAD library for computational
protein design.
The EGAD library is an object-oriented C++ library for conducting
computational protein design. It was developed in the Handel lab by
Arnab Chowdry, Mark Voorhies, Melinda Hanes and myself. The library
supplies classes for common protein design energy terms, such as
Lennard-Jones, Coulombics, generalized Born, and a SASA penalty. Many
of the energy terms implemented are derived from the original EGAD
stand-alone executable, developed by Navin Pokala. EGAD_lib also
provides classes for popular search algorithms, such as Dead End
Elimination and Monte Carlo. For a full description of EGAD_lib, as
well as the results of testing EGAD_lib on several common protein
design tasks (core repacks and calculation of changes in
protein-protein complex affinity due to mutation), please see our paper
in the Journal of Computational Chemistry. Also, further description,
documentation, source code and example problems are provided on the
EGAD_lib website.
The EGAD_lib website:
egad.ucsd.edu/egad
The EGAD developers. From left to right: Arnab
Chowdry, Mark Voorhies, Navin Pokala, Melinda Hanes, Kim Reynolds
EGADView PyMOL plugin.
A PyMOL interface to EGADLib. This plugin provides a GUI interface to
energy table calculation. The goal is to allow visualization of the
EGAD-calculated energies in the context of a protein structure. It will
display the energy tables as color coded maps, which will allow linked
selection of high and low energy parts of the protein structure in
PyMOL. A histogram plot of pairwise interaction energies is also
available.
Download: PyEGADView
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useful links:
Molsoft,
LLC
PyMOL
The PyMOL wiki
The GPCRdb
The
White lab's list of crystallized membrane proteins
The PDB
Dan Reynolds'
web page |
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