Alexander S. Bayden
|Ph.D.||University of Pittsburgh||2000-2005||Chemistry||3.84|
|B.S.||Virginia Polytechnic Institute & State University||1996-2000||Chemistry||3.83|
Computer-aided drug design
Molecular modeling of peptides and peptide-protein interactions
Virtual library design
Developing software for stabilizing 3D structure of peptides
Developing methods to for predicting ADME/Tox properties of peptides
Developing software for determining which water molecules should be displaced from protein active sites
Developing scripts that make structure-based methods easier to use
Postdoctoral Research at AstraZeneca / Randstad (Mentor – Dr. Michelle L. Lamb)
Developing methods and implementing computational chemistry workflows for investigating the role of water in protein-ligand interactions
Developing web application for running water-related calculations on a Linux cluster
Running water-related calculations for computational chemists
Postdoctoral Research at Virginia Commonwealth University (Mentor – Prof. Glen E. Kellogg)
Modeling of Biological Systems
Studying the mechanism of p53 tetramerization
Modeling interactions between SHP2 and EGFR proteins with respect to radiation sensitivity
Docking / 3D Database Searching
Design of pentapeptide inhibitors for O-acetylserine sulfhydrylase
In-silico screening for inhibitors of parainfluenza fusion protein
Docking of small-molecule probes to TrmD, a promising antibiotic target
Computational hydropathic analysis of polysubstituted pyrroles as potential tubulin inhibitors
Developing a method for predicting selectivity in nitration of tyrosines
Automation of analysis for docking results and molecular dynamics trajectories
Developing web applications for studying various aspects of energetics of binding in protein-ligand complexes
Developing of an intuitive GUI for the HINT program
Developing CoMBASA, a tool for pharmacophore analysis and visualization
Graduate and Undergraduate Research at the University of Pittsburgh
(Graduate Academic Advisor – Prof. Kenneth D. Jordan)
Providing computational support for a synthetic group by modeling organometallic catalysis in the synthesis of a promising antibacterial agent, Guanacastepene A
Development of global optimization algorithms
Reimplementing a program for analysis of photoacoustic calorimetry signals to run on Windows
Citizenship: U.S. Citizen
MOLECULAR MODELING SKILLS
Experience with molecular modeling
Skills in both QM and MM methods
Estimation of Gibbs free energies of non-covalent interactions
Modeling water in biological systems
Docking / Virtual screening / 3D pharmacophore searching
Experience with modeling and visualization packages
Maestro, Glide, Prime
MOE, YASARA, Sybyl, CMDInventus, GOLD, HINT, Gaussian, GAMESS, VASP, CAChe, Hyperchem, OpenBabel
Spotfire, DataWarrior, Vortex, CMDnavigator, nQuery
Non-stochastic optimization algorithms
Global optimization algorithms
Algorithms for matrix manipulation
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 or OS X machine under my administration
Windows 10 / 8.1 / 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
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
Understanding of crystallography and the drug development process
Taught analytical chemistry lab and physical chemistry lab
2000 Graduate Excellence Fellowship 2000 Chair’s Scholar Grant
2000 Hypercube Scholar Award 1997-2000 Bilisoly Scholarship
2000 Virginia Polytechnic Institute and State University Academic Excellence Award
1996 National Honor Society
Quantitative 800 (perfect) Analytical 720 Verbal 500 Chemistry 820
2016-Present Senior Research Scientist, Computational Chemistry at IDEAYA Biosciences
Computer-aided drug design
2013-2016 Computational Chemist at CMDBioscience
Molecular modeling of peptides / scientific programming (See pg. 1)
2011-2013 Postdoctoral Fellow at Randstad / AstraZeneca R&D Boston
Molecular modeling / scientific programming (See pg. 1)
2006-2010 Postdoctoral Fellow / Lab & Research Specialist II
at the Virginia Commonwealth University Medicinal Chemistry Department
Computational medicinal chemistry research and scientific application development (See pg 1)
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 H2 on the Si(100) surface
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 the 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 training for administrative assistants and junior web team members
Provided recommendations for software purchases
Worked with another team of developers to completely redesign the site
2003 Temporarily took over the duties of system administrator for the Chemistry Department’s Windows computers at the University of Pittsburgh
2000-2002 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
Diller, K. I.; Bayden, A. S.; Audie, J.; Diller, D. J. PeptideNavigator: An interactive tool for exploring large and complex data sets generated during peptide-based drug design projects. Submitted to Comp. in Biol. and Med.
Spyrakis, F.; Ahmed, M. H.; Bayden, A. S.; Cozzini, P.; Mozzarelli, A.; Kellogg, G. E. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J. Med. Chem., 2017, 60, 6781-6827.
Bayden, A. S.; Gomez, E. F.; Audie, J.; Chakravorty, D. K; Diller, D. J. A combined cheminformatic and bioinformatic approach to address the proteolytic stability challenge in peptide-based drug discovery. Pept. Sci. 2015, 104, 775-789.
Diller, D. J.; Swanson, J.; Bayden A. S.; Jarosinski, M.; Audie, J. Rational, computer-enabled peptide drug design: principles, methods, applications and future directions. Fut. Med. Chem. 2015, 7, 2173-2193.
Ahmed, M. H.; Amadasi, A.; Bayden, A. S.; Cashman, D. J.; Cozzini, P.; Da, C.; Chen, D. L.; Fornabaio, M.; Koparde, V. N.; Mozzarelli, A.; Parikh, H. I.; Sarkar, A.; Scarsdale, J. N.; Spyrakis, F.; Surface, J. A.; Tripathi, A.; Zaidi, S. A.; Kellogg, G. E. Understanding water and its many roles in biological structure: some ways to exploit a resource for drug discovery. Chapter in Computer-Aided Drug Discovery, Springer, New York, 2015.
Bayden, A. S.; Moustakas, D. T.; Joseph-McCarthy, D.; Lamb, M. L. Evaluating free energies of binding and conservation of crystallographic waters using SZMAP. J. Chem. Inf. and Mod. 2015, 55, 1552-1565.
Spyrakis, F.; Felici, P.; Bayden, A. S.; Salsi, E.; Miggiano, R.; Kellogg, G. E.; Cozzini, P.; Cook, P. F.; Mozzarelli, A. Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase. Biochim. Biophys. Acta, Proteins Proteomics, 2013, 1, 169-181.
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, 749-762.
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. (First two authors contributed equally.)
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. Comput. Aided. 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. Organometallics, 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
Bayden, A. S. CMDwater: An entropy-based tool for assessing the displaceability of crystallographic waters in crystal structures of protein-ligand complexes.
Ahmed, M. H.; Spyrakis, F.; Cozzini, P.; Bayden, A. S.; Mozzarelli A.; Kellogg G. E. The Biochemical, Structural and Energetic Roles of Water: A Largely Untapped Resource for Drug Discovery? invited Perspective for J. Med. Chem.
Relative importance of energy components in CMDwater – a computational tool for making decisions about displacing crystallographic waters during lead optimization. 252nd ACS National Meeting, Philadelphia, PA, 2016.
Three-ring scaffold with rich biological activity but no commercial availability. 252nd ACS National Meeting, Philadelphia, PA, 2016.
CMDwater: A tool for ranking crystallographic waters for displacement during ligand design. 2016 Mid-Atlantic ACS Regional Meeting, Riverdale, NY, 2016.
Solving ADME/Tox Problems in peptide-based drug discovery using descriptor-based technologies. PepTalks 10, Boston, MA, 2016.
Using a combined cheminformatic and bioinformatic approach to address proteolytic stability challenges in peptide-based drug discovery. 250th ACS National Meeting, Boston, MA, 2015.
Using CMDInventus for understanding and solving ADME/Tox issues in peptide-based drug discovery. 2015 ACS Northeast Regional Meeting, Ithaca, NY, 2015.
The development, validation and application of CMDInventus to enable structure-based peptide drug design and discovery. 2015 ACS Northeast Regional Meeting, Ithaca, NY, 2015.
Development, validation and application of various biophysical modules in CMDInventus to enable structure-based peptide drug design and discovery. 2014 ACS Central Regional Meeting, Pittsburgh, PA, 2014.
Towards the implementation of novel computation tools in CMDInventus for understanding and solving ADME/Tox issues in peptide-based drug discovery. TIDES 2014, Providence, RI, 2014.
Crystallographic Waters: to Displace or Not to Displace? 245th ACS National Meeting, New Orleans, LA, 2013.
Drug Discovery Applications of Solvent Mapping with SZMAP. 242nd ACS National Meeting, Denver, CO, 2011.
Bridging radicals and other factors influencing tyrosine nitration.
2nd Biennial Chemical Insights into Biological Processes Symposium, Frederick MD, 2010.
27th 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 ACS 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.
2nd Annual Summit on Systems Biology, Richmond, VA, 2007.
24th 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.
Understanding and solving ADME/Tox issues in peptide-based drug discovery using novel computation tools in CMDInventus. 252nd ACS National Meeting, Philadelphia, PA, 2016.
Modeling cell permeation and proteolytic cleavage of peptides. 2016 Mid-Atlantic ACS Regional Meeting, Riverdale, NY, 2016.
Understanding and solving ADME/Tox issues in peptide-based drug discovery using novel computation tools in CMDInventus. 250th ACS National Meeting, Boston, MA, 2015.
Natural products with the 6-7-5 ring scaffold. 250th ACS National Meeting, Boston, MA, 2015.
Addressing proteolytic stability challenges in peptide-based drug discovery using a combined cheminformatic and bioinformatic approach. 2015 ACS Northeast Regional Meeting, Ithaca, NY, 2015.
Factors influencing selective nitration of tyrosines in proteins. 2015 ACS Northeast Regional Meeting, Ithaca, NY, 2015.
CMDdescriptor – 1D and 3D descriptors for addressing ADME/Tox challenges in peptide-based drug discovery. 2014 ACS Central Regional Meeting, Pittsburgh, PA, 2014.
A scaffold with rich biological activity but no commercial availability. 2014 ACS Central Regional Meeting, Pittsburgh, PA, 2014.
Using modeling to make decisions about displacing crystallographic waters. 2013 ACS Northeast Regional Meeting, New Haven, CT, 2013.
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. 35th Central Regional ACS Meeting, Pittsburgh, PA, 2003.
Reimplementing a program for analysis of photoacoustic calorimetry signals. University of Pittsburgh Chemistry REU Symposium, Pittsburgh, PA, 1999.
Creating Applications with Python-OEChem Workshop, Cambridge, MA, 2011.