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Curriculum Vitae
Alexander S. Bayden

62 Garden Circle
Apt 12
Waltham, MA 02452-6174

Phone:(571) 225-8130
Email:

OBJECTIVE

A molecular modeling or scientific programming position

EDUCATION

RESEARCH

AstraZeneca / Randstad

• Investigating the role of water in protein-ligand interactions
• Creating and testing computational chemistry workflows
• Poviding computational support for lead optimization projects

Postdoctoral Research (Virginia Commonwealth University)

• Molecular Modeling
  • Docking / 3D Database Searching
  • In-silico screening for inhibitors of parainfluenza fusion protein and O-acetylserine sulfhydrylase, a potential antibiotic drug target
  • Docking of small-molecule probes to TrmD, a promising antibiotic target
  • Computational hydropathic analysis of polysubstituted pyrroles as potential tubulin inhibitors
  • Modeling selectivity in nitration of tyrosines caused by ionizing radiation
  • Studying the mechanism of p53 tetramerization
  • Modeling interactions between SHP2 and EGFR proteins with respect to radiation sensitivity
• Python Programming / UNIX scripting
• Automation of analysis for docking results and molecular dynamics trajectories
• Development of a web application that finds the best proton configuration for a protein-ligand complex as well as predicts how ΔG binding changes with pH (see http://hinttools.isbdd.vcu.edu/CT)
• Development of an intuitive GUI for the hint! program
• Development of a web application that finds how easy it is to displace waters from protein active sites (see http://hinttools.isbdd.vcu.edu/WR)
• Development of an improved, more intuitive way to visualize molecular dynamics trajectories
• Development of CoMBASA, a tool for pharmacophore analysis and visualization

Graduate and Undergraduate Research (University of Pittsburgh)

• Providing computational support for a synthetic group by modeling organometallic catalysis in the synthesis of a promising antibacterial agent Guanacastepene A
• Dissertation: "Modeling Organorhodium Catalysis"
• Investigation of adsorption of hydrogen on the Si[100] surface
• Development of global optimization algorithms (C++)
• Reimplementing a program for analysis of photoacoustic calorimetry signals (Visual Basic)

MOLECULAR MODELING SKILLS

• Experience with molecular modeling
• Skills in both QM and MM methods
• Docking / Virtual screening / 3D pharmacophore searching
• QSAR / QSPR
• Estimation of Gibbs free energies of non-covalent interactions
• Experience with modeling and visualization packages
• OpenEye
• VIDA, SZMAP
• Schrödinger
• Maestro, Glide, Prime, Pymol
• Other
• Sybyl, MOE, GOLD, HINT, Gaussian 98/03, VASP, CAChe, Hyperchem, GAMESS, Cerius2, OpenBabel, gOpenMol, XMakeMol, kmovisto

COMPUTER ENVIRONMENT

• Programming
• Python, C/C++ with MPI, SQL, Basic/Visual Basic, Pascal
• ASP.NET, HTML, VRML, JavaScript
• Algorithms skills
• Deterministic optimization algorithms
• Global optimization algorithms
• Algorithms for matrix manipulation
• Sorting algorithms
• Strong skills in algorithm analysis
• Computer administration skills
• UNIX (Linux and OS X as an administrator, IRIX / AIX / Solaris / BSD as a user)
• Security has never been breached on a single Linux machine under my administration
• Windows 7 / Vista / XP / 2000 / ME / 9X / 3.1 / CE, DOS
• Administered a Windows 2000-based web server with over forty user accounts for years without a single security breach
• Solved network problems arising from malicious attacks
• Hardware
• Participated in building and maintaining clusters for high-performance computing
• Repaired , built and upgraded PCs, Macintoshes, PDAs, GPS devices and cell phones
• Recovered data from damaged drives

CHEMISTRY UNIQUE SYSTEMS

• Understanding of the drug development process
• Basic organic and inorganic synthetic techniques
• Taught analytical chemistry lab and physical chemistry lab
• Did it all and taught it all, from casting ion-selective membranes to operating an STM

EMPLOYMENT

• 2011-Present Postdoc at AstaZeneca / Randstad
  • Investigated the role of water in protein-ligand interactions
  • Created and tested computational chemistry workflows


• 2006-2010 Postdoc at the Virginia Commonwealth University Medicinal Chemistry Department
• Computational medicinal chemistry research and scientific software development
• Wrote grant applications
• Some server administration
• Training collaborators at the University of Parma, Italy to use software developed at Virginia Commonwealth University


• 2006 Prototyped a financial web site for Russia House International, Inc.
• Project completed successfully under strict time constraints


• 2006 Ran a computer repair / data recovery business


• 1999-2005 Employment at the University of Pittsburgh
• 2000-2005 Research Assistant
• Successfully developed global optimization algorithms and implemented them in C++
• Provided computational support for the following projects:
• Rh-based synthesis of combinatorial libraries and antimicrobial agents
• Modeling adsorption of hydrogen on the Si[100] surface
• Communication
• Trained new group members in molecular modeling and algorithm development
• Conducted presentations about the results and recent developments in the field
• Wrote publications and applications for grants
• 2002-2005 Maintained Chemistry Department's web site at the University of Pittsburgh
• Created and updated relational databases
• Created and updated web interfaces for these databases using ASP.#
• Conducted maintenance on the web server
• Interviewed people and wrote news stories
• Provided recommendations for software purchases
• Worked with another team of developers to redesign the site style
• 2003 Temporarily took over the duties of system administrator for the Chemistry Department's Windows computers at the University of Pittsburgh
• 2000-2001 Taught general chemistry recitation, analytical chemistry lab and physical chemistry lab
• Besides teaching, duties included operating and troubleshooting instruments
• 1999 University of Pittsburgh REU Program
• Successfully redesigned and reimplemented a program for analysis of photoacoustic calorimetry signals
• Interacted with users to determine the requirements and new features for the upgraded program
• Converted a QuickBasic program into Visual Basic
• Wrote documentation, performed installations and trained users

PUBLICATIONS

Printed in Journals

• Bayden, A. S.; Yakovlev, V. A.; Graves, P. R.; Kellogg, G. E.; Mikkelsen, R. B. Factors Influencing Tyrosine Nitration – Structure-Based Predictive Models. Free Rad. Biol. & Med. 2011, 50, 749-62.
• Yakovlev, V. A.; Bayden, A. S.; Graves, P. A.; Kellogg, G. E.; Mikkelsen, R. B. Nitration of the Tumor Suppressor Protein p53 at Tyrosine 327 Promotes p53 Oligomerization and Activation. Biochemistry, 2010, 49, 5331-5339.
• Salsi, E.; Bayden, A. S.; Spyrakis, F.; Amadasi, A.; Campanini, B.; Bettati, S.; Dodatko, T.; Cozzini, P.; Kellogg, G. E.; Cook, P. F.; Roderick, S. L.; Mozzarelli, A. Design of O-acetylserine sulfhydrylase inhibitors by mimicking Nature. J. Med. Chem. 2010, 53, 345-356.
• Bayden, A. S.; Fornabaio, M; Scarsdale, N. J.; Kellogg, G. E. Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. J. Comp. Aid. Mol. Des., 2009, 23, 621-632.
• Bayden, A. S.; Brummond, K. M.; Jordan, K. D. Computational Insight Concerning Catalytic Decision Points of the Transition Metal Catalyzed [2 + 2 + 1] Cyclocarbonylation Reaction of Allenes. Orgtanometallics, 2006, 25, 5204-5206.
• Bayden, A. S.; Jordan, K. D. Use of extended dimensions in global optimization. Chem. Phys. Lett., 2004, 385, 101-104.

Manuscripts in Preparation

• Tripathi, A.; Mosier, P.; Bayden, A. S.; Da, C.;Kellogg, G. E. CoMBASA: A New Complementary Map-Based Active Site Analysis Tool for Determining Receptor-Based Pharmacophore.

Acknowleged in Journal Articles

• Sarkar, A.; Kellogg, G. E. Hydrophobicity - Shake Flasks, Protein Folding and Drug Discovery. Current Topics in Medicinal Chemistry, 2010, 10, 67-83.
• Tripathi, A.; Fornabaio, M.; Kellogg, G. E.; Gupton, J. T.; Gewirtz, D. A.; Yeudall, W. A.; Vega, N. E.; Mooberry, S. L. Docking and Hydropathic Scoring of Polysubstituted Pyrrole Compounds with Anti-Tubulin Activity. Bioorganic & Medicinal Chemistry, 2008, 16, 2235-2242.

POSTERS

• Drug Discovery Applications of Solvent Mapping with SZMAP. 242nd American Chemical Society National Meeting, Denver, CO, 2011.
• Bridging radicals and other factors influencing tyrosine nitration.
  • 2^nd Biennial Chemical Insights into Biological Processes Symposium, Frederick, MD, 2010.
  • 27^th Annual Daniel T. Watts Research Poster Symposium, Richmond, VA, 2010.
• Predicting Specificity for Selective Nitration of Tyrosines. Biotech-After-Hours, Richmond, VA, 2009.
• Novel Applications of Python in Computational Chemistry Workflows. CUP X, Santa Fe, NM, 2009.
• Applying Computational Titration to Selective Nitration of Tyrosines. 236th American Chemical Society National Meeting, Philadelphia , PA, 2008.
• Modeling Interactions of Potential Antibiotic Targets OASS A and OASS B with Inhibitory Peptides. 25th Annual Daniel T. Watts Research Poster Symposium, Richmond, VA, 2008.
• Design and Implementation of the Computational Titration Biomacromolecular Analysis as a Web-enabled Online Modeling Tool.
• 2^nd Annual Summit on Systems Biology, Richmond, VA, 2007.
• 24^th Annual Daniel T. Watts Research Poster Symposium, Richmond, VA, 2007.
• Modeling Organometallic Catalysis. University of Pittsburgh Department of Chemistry Graduate Student Research Showcase Poster Session, Pittsburgh, PA, 2004.
• Theoretical Study of the Si(100) Surface.
• University of Pittsburgh Department of Chemistry Graduate Student Research Showcase Poster Session , Pittsburgh, PA, 2003.
• University of Pittsburgh Computer Science Day , Pittsburgh, PA, 2003.
• Dimensional Strategies in Barrier Avoiding Minimization Algorithms. American Conference on Theoretical Chemistry, Champion, PA, 2001.

Posters Presented By Others

• Salsi, E.; Spyrakis, F.; Bayden, A.; Amadasi, A.; Campanini, B.; Bettati, S.; Dodatko, T.; Cozzini, P.; Kellogg, G. E.; Cook, P. F; Roderick, S. L.; Mozzarelli, A. Identification of inhibitors for bacterial O- acetylserine sulfhydrylase-A and -B isozymes via in silico screening of a biased pentapeptide library and in vitro validation. Proteine 2010, Parma, Italy, 2010.
• Spyrakis, F.; Salsi, E.; Bayden, A.; Amadasi, A.; Campanini, B.; Bettati, S.; Dodatko, T.; Cozzini, P.; Kellogg, G.E.; Cook, P.F; Roderick, S. L.; Mozzarelli, A. Identification of inhibitors of O-acetylserine sulfhydrylase via virtual and experimental screening of a biased pentapeptide library. Therapeutic Applications of Computational Biology and Chemistry 2010, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2010.
• Kellogg, G. E.; Tripathi, A.; Sarkar, A.; Surface, J. A.; Bayden, A. S.; Amadasi, A.; Mozzarelli, A.; Spyrakis, F.; Cozzini, P. In Search of Entropy, Site Flexibility, Water and Other Cool Stuff. Experiment Meets Modeling: Where Are We Now, Where Are We Going, Computer Aided Drug Design Gordon Conference, Tilton, NH, 2009.
• Salsi, E.; Amadasi, A.; Bayden, A.; Campanini, B.; Bettati, S.; Kellog, G. E.; Cozzini, P.; Cook P. F., Mozzarelli,A . Interaction Between Serine Acetyltransferase and O-Acetyserine Sulfhydrylase: Kinetics and Design of Potential Bectericides. 22nd Symposium of The Protein Society, San Diego, CA, 2008.

ORAL PRESENTATIONS

• Computational Titration Institute for Structural Biology and Drug Discovery of Virginia Commonwealth University Student Seminar Series, Richmond, VA, 2008.
• Dimensional strategies in barrier avoiding minimization algorithms. 35^th Central Regional American Chemical Society Meeting, Pittsburgh, PA, 2003.
• Reimplementing a program for analysis of photoacoustic calorimetry signals. University of Pittsburgh Chemistry REU Symposium, Pittsburgh, PA, 1999.

SPECIAL RECOGNITION

• 2000 Virginia Polytechnic Institute and State University Academic Excellence Award
• 2000 Graduate Excellence Fellowship
• 2000 Chair's Scholar Grant
• 2000 Hypercube Scholar Award
• 1997-2000 Bilisoly Scholarship
• 1996 National Honor Society

GRE SCORES

Verbal 500      Quantitative 800 (perfect)      Analytical 720      Chemistry 820

OTHER INFORMATION

• Citizenship: U.S. citizen
• References available upon request