Professional Experience of William Michael "Mike" Carson:
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Developed the UAB bioinformatics portion of the funded UAB/UGa
Protein Structure Initiative grant application to the NIH.
The Southeast Collaboratory for Structural Genomics (www.secsg.org)
was awarded one of the seven pilot center grants nationwide in 2000.
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Led the Bioinformatics Team of the Structural Genomics of
Caenorhabditis elegans project at UAB. Developed a custom LIMS system
for experimental results from cloning through crystallography
and a web site to make all data available to the public (sgce.cbse.uab.edu).
We were the first structural genomics group to have
a protein production database online.
Our development efforts are summarized in "SGCEdb: a flexible database
and web interface integrating experimental results and analysis for
structural genomics focusing on Caenorhabditis elegans"
DH Johnson, J Tsao, M Luo and M Carson (2006)
Nucl. Acids Res. 34:D471-D474.
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Created methodology to prioritize targets, focusing on unique protein folds.
A unique target solved highlighting the groups methods is
"Crystal Structure of the Cytoskeleton-associated Protein
Glycine-rich (CAP-Gly) Domain."
S Li, J Finley, ZJ Liu, SH Qiu, H Chen, CH Luan, M Carson,
J Tsao, D Johnson, G Lin, J Zhao, W Thomas, LA Nagy, B Sha,
LJ DeLucas, BC Wang, and M Luo (2002)
J.Biol.Chem. 277:48596-48601.
Models were also created suggesting a mode of binding to the cytoskeleton.
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Represented the group's efforts with an invited talk
"Visualizing a Can of Worms: The SGCE Database"
at the IBM Symposium on Structural Genomics in 2002
and with a poster presentation at the 2003
Biophysical Society Annual Meeting.
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Analyzed and illustrated protein structures as they were determined,
most in collaboration with Henry Symersky and Norbert Schormann.
Some favorites are
"Structural Genomics of Caenorhabditis elegans:
Crystal Structure of the Tropomodulin C-Terminal Domain."
S Lu, J Symersky, S Li, M Carson, L Chen, E Meehan, and M Luo (2004)
Proteins 53:944-946 (an unknown fold when the study began)
and the
"Structural Genomics of Caenorhabditis elegans:
Crystal Structure of Calmodulin"
J Symersky, G Lin, S Li, M Carson, N Schormann, and M Luo (2003)
Proteins 53:947-949 (done for methodological development).
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The SGCE group performed expression experiments on more genes from an
individual organism than had ever been done.
"High-Throughput Expression of C. elegans Proteins."
CH Luan, S Qiu, JB Finley, M Carson, RJ Gray, W Huang, D Johnson, J Tsao,
J Reboul, P Vaglio, DE Hill, M Vidal, LJ DeLucas and M Luo (2004)
Genome Research 14:2102-2110. This also includes our
first efforts to mine the data.
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Monitored the quality and Protein Data Bank deposition of all
of the SGCE structures. Data presented in
"A test of enhancing model accuracy in high-throughput crystallography"
WB Arendall III, W Tempel, JS Richardson, W Zhou, S Wang, IW Davis,
ZJ Lu, JP Rose, WM Carson, M Luo, DC Richardson and BC Wang (2005)
J. of Structural and Functional Genomics 6:1-11.
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Wrote the bioinformatics portions for follow-up specialized center
proposals for a center for eucaryotic structural genomics
and for a center for membrane protein structural genomics.
-
Developed and taught a complete course sequence
in bioinformatics at UAB:
CS640 Bioinformatics I (sgce.cbse.uab.edu/carson/cs640)
CS641 Bioinformatics II (sgce.cbse.uab.edu/carson/cs641)
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Current work focuses on improving chances for successful crystallization
and hence structural determination. The 'infac' program of Charlie Carter
has been ported to our computers for incomplete factorial screening
in collaboration with Lisa Nagy.
Neural Networks to predict improved crystallization are being developed
by David Johnson, now under my mentorship as a PhD student in BME,
in collaboration with Larry DeLucas.
Data mining of the reported crystal conditions of known PDB structures
is underway.
-
Modeling of the binding of DMSO to the NADS enzyme
in collaboration with Christie Brouillette.
"DMSO at 2.5% (v/v) Alters the Structural Cooperativity and
Unfolding Mechanism of Dimeric Bacterial NAD Synthetase."
ZW Yang, SW Tendian, WM Carson, WJ Brouillette,
LJ. DeLucas, and CG Brouillette (2004)
Protein Science 13:830-841.
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Description of the interactions in crucial Chagas' disease proteins
in collaboration with Debasish Chattopadhyay.
"Crystal structure of Trypanosoma cruzi pteridine reductase 2
in complex with a substrate and an inhibitor"
N Schormann, B Pal, O Senkovich, M Carson, A Howard,
C Smith, L DeLucas and D Chattopadhyay (2005)
J. Struct. Biol. 152:64-75.
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Modeling and analysis of bacterial adhesion proteins
in collaboration with Champion Deivanayagam.
"Crystal Structure of Clumping Factor A: a Fibrinogen-Binding MSCRAMM
of Staphylococcus aureus."
CCS Deivanayagam, ER Wann, W Chen, M Carson, CS Ramarao, KR Rajashankar,
M Hook, and SVL Narayana (2002)
EMBO Journal 21:6660-6672.
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Molecular modeling and development of novel representations of
lipoproteins in collaboration with Krishna Murthy.
"Structures of Apolipoprotein A-II and a Lipid-Surrogate Complex
Provide Insights into Apolipoprotein-Lipid Interactions."
MS Kumar, M Carson, MM Hussain, and HMK Murthy (2002)
Biochemistry 41:11681-11691.
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Preliminary map fitting and refinement of human PIMT in
collaboration with Craig Smith and Debasish Chattopadhyay.
Investigated the geometry of S-adenosyl methionine through study of
small molecule in the CSSD and modeling the
catalysis of protein substrates.
"Crystal Structure of Human L-Isoaspartyl-O-Methyltransferase
with S-Adenosyl Homocysteine at 1.5A Resolution and Modeling
of an Isoaspartyl Containing Peptide at the Active Site."
CD Smith, M Carson, AM Friedman, MM Skinner, L DeLucas, L Chantalat,
L Weiss, T Shirasawa and D Chattopadhyay (2002)
Protein Science 11:625-635.
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Collaboration on the NSF grant application "Interactive Concepts
in Biotechnology" with Anna Holmes at UAH for a regional
web-based educational and research tool.
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Structure determination and modeling interactions of malarial
cell-signaling proteins. D Chattopadhyay, G Langsley, M Carson, R
Recacha, L. DeLucas and CD Smith (2000) Structure of the
nucleotide-binding domain of Plasmodium falciparum Rab6 in the
GDP-bound form. Acta CrystD56:937-944 (and
cover picture).
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Refinement of the crystal structure of the anti-Interferon gamma
receptor FAB fragment and modeling of binding to its receptor in
collaboration with Dr. Mark Walter (manuscript in preparation) .
-
Drug design projects against malarial targets with Dr. Chattopadhyay
and collaborators at Walter Reed. Drug design, modeling, and an SBIR
grant submission with Drs. Raj Singh and Sam Ananthan on cancer-related
matrix metallo-proteins.
-
Modeling of viral capsid proteins in collaboration with scientists in
the UAB AIDS center (Dr. P.Priveledge) and the UAB Gene Therapy Center
(Drs. R. Alemany/D.Curiel).
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Analysis and modeling of binding proteins in collaboration with
Champion Deivanayagam and the Narayana/Hook groups. CCS Deivanayagam,
RL Rich, M Carson, RT Owens, S Danthuluri, T Bice, M Hook and SVL Narayana
(2000) Novel Fold and Assembly of the Repetitive B Region of the
Staphylococcus aureus Collagen-binding Surface Protein.
Structure 8:67-78;
RL Rich, CCS Deivanayagam, RT Owens, M Carson, A Hook, D Moore, VWC
Yang, SVL Narayana and M Hook (1999) Trench-shaped Binding Sites
Promote Multiple Classes of Interactions between Collagen and the
Adherence Receptors, alpha-1 beta-1 Integrin and S.aureus
Cna MSCRAMM. J.Biol.Chem 274:24906-24913;
CCS Deivanayagam, M Carson, A Thotakura, SVL Narayana and RS
Chodavarapu (2000) The Crystal Structure of FKBP12.6 in Complex with
Rapamycin. Acta Cryst D56:266-271 (and cover
picture).
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Collaboration with Drs. Rosario Recacha, Debasish Chattopadhyay and
Robert Wood Johnson scientists in the refinement, analysis, and
illustration of important proteases in complex with inhibitors. R
Recacha, M Carson, MJ Costanzo, LJ DeLucas and D Chattopadhyay (2000)
Structure of the RWJ-51438-Human alpha-Thrombin Complex at 1.7A, Acta
Cryst D56:937-944; R Recacha, M Carson, MJ Costanzo, B
Maryanoff, LJ DeLucas and D Chattopadhyay (1999) Structure of the
RWJ-51084-Bovine Pancreatic beta-Trypsin Complex at 1.8A. Acta
Cryst D55: 1785-1791.
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Modeling and analysis work on complement proteins in collaboration
with Narayana's group. H Jing, Y Xu, M Carson, D Moore, KJ Macon, JE
Volanakis and SVL Narayana (2000) New Structural Motifs on the
Chymotrypsin Fold and Their Potential Roles in Complement Factor B.
EMBO Journal 19:164-173.
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Member of the CMC/BioCryst drug design team for Factor D.
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Member of the CMC/BioCryst drug design team for Neuraminidase.
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Collaboration with various CMC/UAB members on inhibitor design against
a variety of enzymes involved in disease. Poster presented at the
1997 DARPA meeting on Emerging Infections and Antimicrobial Resistance:
"Structure Based Strategy for Developing Inhibitors of NAD
Synthetase", WJ Brouillette, DD Muccio, W Cristofoli, M Carson,
R Singh, MJ Jedrzejas and Y Devedjiev.
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Modeling and analysis work on several projects in collaboration with
with Narayana's group. J Symersky, JM Patti, M Carson, M Teale, D
Moore, L Jin, LJ DeLucas, M Hook and SVL Narayana (1997) The
Collagen-binding Domain of Staphylococcus aureus Adhesin. Nature
Struct.Biol. 4:833-838.; G Lin, D Chattopadhyay,
M Maki, KKW Wang, M Carson, L Jin, P Yuen, E Takano,
M Hatanaka, LJ DeLucas and SVL Narayana (1997) Crystal
Structure of Calcium Bound Domain VI of Calpain at 1.9A Resolution and
its Role in Enzyme Assembly, Regulation, and Inhibitor Binding. Nature
Struct.Biol. 4:539-547.; A Agrawal, SJ Lee, M
Carson, SVL Narayana, TJ Greenhough and JE Volanakis (1997)
Site-directed Mutagenesis of the Phosphocholine-binding Site of Human
C-Reactive Protein: Role of Thr76 and Trp67.
J. Immunol. 158:345-350.
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Calculation of binding energies of various enzyme/drug complex
structures determined by crystallography and comparisons with the
observed constants. M Carson, Z Yang, YS Babu and JA Montgomery
(1994) "Calculation of Relative Binding Affinities of Purine
Nucleoside Phosphorylase Inhibitors"
Acta Cryst. D51:536-540.
Author of the book chapter describing the PNP work. YS Babu, JA
Montgomery, CE Bugg, M. Carson, SVL Narayana, W.J. Cook, SE
Ealick, WC Guida, MD Erion, and JA Secrist III (1997)
"Design of PNP Inhibitors" in: Structure Based Drug
Design, Ch.5 pp.151-169, P. Veerapandian, ed, Marcel Decker.
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Presentation of "Error Detection in Protein Crystal Structures
with Ribbons++" at the 1994 annual meeting of the American
Crystallographic Association.
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Creation of a model of neuraminidase by modeling from estimated
C-alpha positions of a related molecule and molecular replacement with
native crystal diffraction data. Phases from this model and X-ray
difference data correctly placed the bound substrate in the active
site. Subsequent refinement of neuramididase to 2.5 A, R = 19.
P Bossart-Whitaker, M Carson, YS Babu, CD Smith, WG Laver and
GM Air (1993) "Three-Dimensional Structure of Influenza A N9
Neuraminidase and its Complex with the Inhibitor 2-deoxy
2,3-dehydro-N-acetyl Neuraminic Acid"
J.Mol.Biol. 232:1069-1083.
Structure-based inhibitor design based on the influenza virus
neuraminidase and its complex with a transition state analog inhibitor.
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Initial model building, refinement, and analysis of the structure of
human interferon-gamma to 3.5 A resolution. The preliminary structure
appeared in Science: SE Ealick, WJ Cook, S Vijay-Kumar,
M Carson, TL Nagabhushan, PP Trotta and CE Bugg (1991)
"Three-Dimensional Structure of Recombinant Human
Interferon-gamma" Science 252:698-702.
Investigation of a number of refinement strategies for human
gamma-interferon.
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Solution of the human complement protein Factor-D by modeling and
molecular replacement. Invited talk "Modeling a Protein from
Homology: Comparison with Experimental Results" at the 1991
University of Iowa conference on computer visualization and imaging.
The structure has subsequently been refined to high resolution. SVL
Narayana, M Carson, O El-Kabbani, JM Kilpatrick, D Moore, X Chen,
CE Bugg, JE Volanakis and LJ DeLucas (1994) "Structure of
Human Factor D, a Complement System Protein at 2.0 A Resolution"
J.Mol.Biol. 235:695-708.
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Detailed comparison of the preliminary models of Factor-D with the
final refined structure. Calibration of error detection techniques in
models. M Carson et al (1994) Acta Cryst. D50:900-909.
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Refinement of SOD with peroxynitrite. Comparison of native and nitrated
structures. "Crystal Structure of the Reaction Product of
Peroxynitrite with Bovine Cu,Zn Superoxide Dismutase" C Smith, M
Carson, M van der Woerd, H Ischiropolous, J Chen and J Beckman
(1992) Arch.Biochem. Biophys. 299:350-355. Some
speculation of the biological importance of the system. JS Beckman,
M Carson, CD Smith and WH Koppenol (1993) "ALS, SOD and
peroxynitrite." Nature 364:584.
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Theoretical analysis of autoantigenic protein structure. "Long
charge-rich alpha-helices in systemic autoantigens" J Dohlman,
A Lupas and M Carson (1993)
Biochem.Biophys.Res.Comm. 195:686-696.
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Analysis and comparison of diffraction intensities of earth-grown and
space-grown crystals of insulin in collaboration with C Smith,
M Long and C Bugg.
LJ DeLucas et al (1994) "Recent Results and New
Hardware Developments for Protein Crystal Growth in Microgravity."
J.Crystal Growth 135:183-195.
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Refinement of scorpion toxin Variant-3 to 1.2 A. Parallelization of
PROLSQ for 240 GTX. Comparison of XPLOR and PROLSQ refinement.
"Structure of Scorpion Toxin Variant-3 at 1.2 A Resolution"
B Zhao, M Carson, SE Ealick and CE Bugg (1992) J.Mol.Biol.
227:239-252.
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Solution of diubiquitin by molecular replacement and preliminary
refinement. "Structure of a Diubiquitin Conjugate and a Model for
Interaction with Ubiquitin-conjugating Enzyme (E2)" WJ Cook,
LC Jeffrey, M Carson, Z Chen and CM Pickart (1992) J.Biol.Chem.
12:11-13.
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Creation of a Python-based GUI for all ribbons utilities common
to the Unix, Linux, Mac, and PC version.
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Porting of ribbons to the Mac, thanks to a loaner from Apple.
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Conversion of ribbons to a native Windows PC version with Jun Dai.
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Development of an STL object-based prototype gibbons, the
successor to ribbons. Ribbons has been compiled under
several linux flavors and will be made open-source.
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Creation of an algorithm and a web server to create full-atom RNA
models from phosphate positions (www.cmc.uab.edu/P2rna).
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Development of a suite of programs to superimpose and determine domain
relationships in IGG-like proteins.
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Ongoing development of the popular molecular display program
ribbons (sgce.cbse.uab.edu/ribbons), and contribution of
the invited chapter: M. Carson (1997) Ribbons. Methods in
Enzymology: Macromolecular Crystallography, 277:493-505,
R.M. Sweet and C.W. Carter, eds, Academic Press.
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1996 Silicon Graphics Visual Computing Awards.
(www.sgi.com/Fun/free/96_contest and published in the Spring '97
issue 'IRIS Universe', Vol 39, pp 12-13.) The category winner in
Computer-Aided Chemistry entitled "The Mother of All
Molecules" was created using Ribbons 2.0 software and rendered
with Wavefront's Personal Visualizer.
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Presentation of "Wavelets and Molecular Structure" at the
1995 annual meeting of the Molecular Graphics Society. Investigations
of applications of the wavelet transform to molecular modeling
problems.
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Creation of a complete on-line hypertext manual/help screens in HTML
format for ribbons 2.6.
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Implementation of SoftDock, a version of the Jiang and Kim algorithm
for the automated docking of molecules.
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Acceptance of three images made using my programs by the highly
competitive SIGGRAPH '94 slide set showcasing the best computer
graphics of the last year.
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Organization of R++ Software Design Team to develop an object-oriented
approach to re-fitting protein structures to experimental data.
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Development of a protocol to identify potential errors in atomic models
produced by crystallographic analysis.
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Invention of DNurbs --- a novel representations of nucleic acids. M.
Carson and Z. Yang (1994) DNurbs: DNA modeled with NURBS. J.Mol.Graphics
12:178-184.
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Presentation of Ribbons++ prototype at the 1993 annual meeting of the
Molecular Graphics Society.
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Implementation of SoftDock procedure to screen databases of potential
drug molecules.
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Licensing of the Ribbons 2.0 software to over 150 sites worldwide.
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Enhancement of a local version of FRODO, "Atom", to allow
more rapid rebuilding of preliminary atomic models into the electron
density maps.
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Automatic generation of complete atomic models from initial C-alpha
coordinates. This unpublished method has been used to generate most of
the starting models for structural refinement in this lab.
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Re-engineering of Bhat's OMITMAP program from a VAX-specific version to
a general form suitable for VAX, CRAY, or UNIX workstations.
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Porting of SPRUCE to the AT&T Pixel Machine/Sun system in
collaboration with BioCryst. The software exhibited at SigGraph
'88, and a plaque awarded by AT&T for outstanding contributions.
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Development of an elegant algorithm for the display of ribbon models of
macromolecules. Illustrations from the original "ribbon"
program appeared as covers on both Science and Nature.
The software companies TRIPOS and Polygen incorporated the algorithm
into their molecular modeling packages.
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Mapping of enzyme active sites for rational drug design. (Unpublished
results in collaboration with BioCryst and Ciba-Geigy.)
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Porting and enhancement of GRINCH, the UNC program for the preliminary
interpretation of protein electron density maps, to run on
PS300/VAX/VMS and SGI-IRIS/UNIX environments.
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Energy refinement and molecular dynamics simulations.
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Modeling of protein/water interactions.
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Software development, testing, and documentation of the CEDAR (Crystal
Energy, Dynamics and Refinement) program. The conversion of J. Hermans'
IBM Fortran code into UNIX rational Fortran with macros allowed
the code to be ported to a variety of machines. Hermans' group
published several interesting free energy perturbation studies of
peptides in water running the code on a CRAY. This software was
incorporated into the XTAL package of programs in collaboration
with K. Watenpaugh.
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Software development of a C language interface, SPRUCE, to visualize
the results of CEDAR on an Evans & Sutherland PS300. One of the
first systems to allow the viewing of molecular dynamics animations.
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Collaboration with the UNC GRIP project in molecular graphics. Assisted
with the production of an interface between the PROFET computer network
and the UNC system.
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Data reduction of "partial" reflections and the incorporation
of procedures to analyze partials from X-ray data into the MPI PROTEIN
series of programs.
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Synchrotron data collection.
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X-ray crystallographic analysis of ascorbate oxidase.
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Dissertation on the elucidation of the tertiary and quaternary
structure of invertebrate hemoglobins, using single crystal diffraction
and molecular modeling techniques.
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Crystallization experiments with multienzyme complexes.
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Solution of "small molecule" structure of enkephalin fragment.
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Undergraduate/Graduate Biochemistry:
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Carbohydrate analysis.
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Organic synthesis.
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Bacterial enzymology.
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SQL/ Python/ PHP development for structural genomics database and server.
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Microsoft Visual C++ development for pcRibbons.
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SpecTcl/ Python development for utility GUIs.
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Script development for parallelizing jobs on a Linux cluster.
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ANSI C++/Standard Template Library programming on Linux for
gibbons (gnu ribbons).
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Web-based software distribution for the Unix/C++/X/Motif/OpenGL
molecular visualization program ribbons (sgce.cbse.uab.edu/ribbons).
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VRML2.0/ JavaScript/cgi/perl development for an electronic conference
(sgce.cbse.uab.edu/SoundOfSequence).
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HTML and VRML development for the World Wide Web.
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OpenGL graphics programming on SGI and DEC machines.
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C++ programming with the IRIS Inventor 3-D Toolkit.
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PEX/Motif development with the E&S ESV workstation.
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CRAY/UNICOS experience with the Alabama Supercomputer Network.
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STELLAR graphics supercomputer and AT&T Pixel Machine programming.
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CYBER-205 Supercomputer Summer Research Institute attendee.
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SUN/UNIX, IBM/p-system, and Sequent/DYNIX with the CIS department.
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VAX/VMS, SGI-IRIS/UNIX, and E&S MPS and PS300 with the UAB CMC.
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FORTRAN and BASIC on HT11 Heathkit computer. C language driver for
small laboratory plotter.
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PASCAL programming on the Apple.
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VAX/UNIX experience with UNC Computer Science Department.
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VAX/VMS experience with the MPI group.
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BASIC programming for laboratory diffractometer.
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CDC batch processing at the UT Computer Center. Considerable FORTRAN
programming for dissertation work.
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Member of BME Graduate Education Committee.
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Member of the UAB Enabling Technology Laboratory (ETL) use committee,
to allocate time on the large linux cluster in the School of Engineering.
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Manuscript reviewer for Bioinformatics, Acta Crystallographica,
Journal of Molecular Graphics, IEEE Computer Graphics,
IEEE Computational Biology and Bioinformatics.
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Grant reviewer for the American Chemical Society.
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Program presentations for various groups of middle school, high school,
and college science students.
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Assisted Dr. Martin Weiss with the exhibit "Marvelous
Molecules-The Secret of Life" at the New York Hall of Science.
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Wrote the Health Science Foundation funded grant
"Internet 2-Capable Networking for the
Basic Health Sciences Building" to improve networking
infrastructure at UAB.
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Program committee member for the 1991 International Meeting of the
Molecular Graphics Society.
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Organization of the session "Modeling and Visualization" at
the 1989 Carolina Conference on Protein Engineering.
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Organization of the session "Graphics: Art in Science" at the
1988 American Crystallographic Association annual meeting.
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Audit of courses in computer architecture, graphics, data structures,
image processing/pattern recognition, software engineering,
differential geometry, computational geometry, and quantum mechanics.
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Professor:
- Physical Chemistry (senior level).
- Computer Graphics (graduate and undergraduate).
- Scientific Programming in C++ (graduate).
- Bioinformatics I (senior level and graduate).
- Bioinformatics II (graduate).
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Mentor: BME graduate student David Johnson.
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Mentor: CMC graduate students Drs. S.Rowland, B.Zhao, and
P.Bossart-Whitaker.
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Computer and Information Science Committee member:
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PhD dissertation, "Parallel adaptations of stochastic modeling
techniques for computer graphics", M. Wainer (1987)
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Master's thesis, "Crystallographic Information Server", T.
Buckner
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PhD Dissertation, "Hardware-assisted volume rendering", J.
Freund (1997)
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Master's thesis, "Advanced Keyframe User Interface for Quaternion
Animation", H. Graham
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PhD Dissertation, "Third Dimension Object Recognition using Alpha
Shapes", M. Cameron (1999)
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PhD Dissertation, "Morphing Many Polygon Across a Change
in Topology", X. Wu (2003)
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Biochemistry Committee member:
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PhD dissertation, "Computer Modeling of Functional RNAs,
Concentrating on the Small Ribosomal Subunit of E. Coli", M. Van
Loock (2000)
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PhD dissertation, "Structural studies of ribosyl
transferases", T. Bice (2004)
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PhD dissertation, "Design of NAD Synthetase Inhibitors",
S.Weiss, present
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Guest Lecturer: physical biochemistry, protein structure, X-ray
crystallography, molecular modeling, structural databases.
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Instructor: C language programming (undergraduate).
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Instructor: computer graphics (undergraduate).
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Lecturer: general chemistry.
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Head teaching assistant: general chemistry.
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Teaching assistant: organic chemistry laboratory.