Derek J. Cashman, Ph.D.

Curriculum Vitae

Computational Biophysical Chemist with 20 years of post-graduate research experience and 10 years of undergraduate and graduate teaching experience. My specialties are in the realm of structure-based drug design, computer modeling and molecular simulations of proteins and nucleic acids, and 3D printing. The focus of my research is to connect virtual high-throughput screening and docking and scoring and the molecular modeling of protein fluctuations, utilizing molecular dynamics or Monte Carlo simulations, in order to better incorporate protein flexibility into structure-based drug design. Recent experience in this area includes the use of artificial intelligence (Alphafold2) in predicting protein structure. I am highly experienced in the use and parallel programming on High Performance Computing (HPC) systems, including supercomputing clusters such as ORNL’s TITAN and KRAKEN supercomputers. Author of 19 peer-reviewed journal articles and presented research at over 65 regional and national scientific meetings. My teaching experience includes 10 years as the instructor of record for courses in general, organic, biochemistry, and physical chemistry with an emphasis on applications to the pharmaceutical biotechnology and energy. I have also served as a research mentor to 12 undergraduate students and six graduate students, and have served on the M.S. thesis committee for 28 graduate students. I am also involved in the organization of peer-mentoring events and activities, such as advising the student chapter of the American Society of Biochemistry and Molecular Biology, assisting in the organization of seminars and outreach events, and other community service activities.

Education

Ph.D., Pharmaceutical Sciences (Concentration in Medicinal Chemistry)
Virginia Commonwealth University, Richmond, Virginia
December 2003

Dissertation: A Computational Model for Targeting Nucleic Acids: Estimating Changes in Free Energy of Drugs in Complex with RNA and Variable Sequences of DNA. (Advisor: Glen E. Kellogg, Ph.D.)


B.S., Biology (Minor: Chemistry)
Old Dominion University, Norfolk, Virginia
May 1995

Professional Experience

Tennessee Technological University

  • Lecturer (2016 – present)
  • Instructor (2013 – 2016)
  • Instructor of record for biochemistry lecture, biochemistry laboratory, nutritional biochemistry, organic chemistry, physical chemistry, introductory chemistry, and chemistry for the life sciences.
  • Developed novel laboratory curriculum sessions in computational chemistry for students.
  • Advised and mentored 11 undergraduate and served on the thesis committee of 28 graduate students on original research projects related to computational chemistry and molecular biophysics.
  • Mentored high school students in computational chemistry methods as part of the Governor’s School for Emerging Technologies (2015 – 2023).
  • Development of methods for teaching students on the use of artificial intelligence (Alphafold2) in biochemistry research involving proteins and nucleic acid structure predictions.

University of Tennessee at Knoxville / Oak Ridge National Laboratory

  • Performed homology modeling, molecular dynamics, and Monte Carlo simulations of bacterial chemotaxis proteins using bioinformatics, phylogenetic analysis, and experimental data as a guide, resulting in an improved understanding of their overall protein-protein interactions and dynamics.
  • Performed protein-protein docking calculations on bacterial chemotaxis proteins, as well as Ferredoxin and Photosystem I, guided by energy landscape theory, machine learning and experimental data, resulting in potential docked complexes and the characterization of key protein-protein interactions.
  • Advised and mentored graduate and undergraduate students on computational methodology and methods of homology modeling and protein-protein interactions.
  • Taught lectures on biophysical chemistry, computational chemistry, and facilitated discussion sessions on research topics for students in the department.

University of Pittsburgh

  • Simulation of protein systems using molecular dynamics & Monte Carlo methods, including those involved in bacterial chemotaxis and cancer, as part of the development and validation of Library-Based Monte Carlo (LBMC) software. LBMC enables faster sampling of protein configurational dynamics on desktop-capable workstations, providing a tremendous benefit for ensemble docking calculations. http://www.ccbb.pitt.edu/Faculty/zuckerman/software.html
  • Served as the Marketing & Communications Officers of the University of Pittsburgh Postdoctoral Association in 2009. Responsible for coordinating and advertising peer-mentoring events, including a monthly seminar series and an annual poster symposium for other postdoctoral researchers.

Northern Arizona University

  • Construction of homology models, virtual screening, biophysical characterization (ITC, DSC, spectroscopy), and molecular dynamics simulation of elements of telomeric DNA (G-quadruplex, i-Motif), resulting in an improved understanding of the pharmacophore and the identification of potential new lead compounds for cancer research.
  • Served as a mentor for undergraduate and graduate students in the laboratory, educating them on proper laboratory procedure and computational theory and methodology on a variety of research projects.

University of Louisville

  • Postdoctoral Research Fellow, Dr. Jonathan B. Chaires (2004 – 2005)
  • Developed a structural model for the binding of bis-anthracycline compounds to several sequences of double-stranded DNA, resulting in the identification of preferred binding sequences as well as the ability to visualize the pharmacophore of a new and potentially groundbreaking anticancer drug.
  • Assisted with the setup of a state-of-the-art biophysical core facility at the James Graham Brown Cancer Center.

Virginia Commonwealth University

  • Graduate Research & Teaching Assistant, Dr. Glen E. Kellogg (1998 – 2003)
  • Performed a virtual screening analysis of Doxorubicin analogs, including docking and free energy estimation of compounds to variable sequences of DNA, resulting in the identification of several modified compounds with increased affinity towards specific sequences.
  • Performed docking and free energy estimation of aminoglycoside analog binding to 16S ribosomal RNA, resulting in a better understanding of the mechanism by which the compounds interacted in their binding pocket.
  • Taught courses and laboratory sessions in chemistry and biochemistry, as well as computational tutorials and methodologies in QSAR and molecular modeling.
  • Assisted in the development of outreach activities to visiting high school, undergraduate, and graduate students visiting the Virginia Biotechnology Research Park.

Teaching Experience

Tennessee Technological University

  • Introductory Chemistry (CHEM 1010/1020)
  • Chemistry for the Life Sciences (CHEM 1210)
  • Nutritional Biochemistry (CHEM 4500)
  • General Biochemistry (CHEM 4610/5610/4620/5620)
  • Physical Chemistry (CHEM 3510/3520)hysical Chemistry for the Life Sciences (CHEM 3500)
  • Biochemistry Laboratory (CHEM 4650/5650)
  • Special Topics: Quantum Chemistry (CHEM 5970)
  • Advanced Biochemistry (CHEM 6610)
  • Advanced Molecular Modeling (CHEM 6350)
  • Organic Chemistry (CHEM 3010)
  • Special Topics: Chemistry of Beer (CHEM 4970)

University of Tennessee at Knoxville

  • Introduction to Molecular Biophysics (BCMB 420/520/610)
  • Topics in Biochemistry, Biophysics and Molecular Biology (BCMB 601)

Virginia Commonwealth University

  • Pharmaceutical Analysis Laboratory (MEDC 602)
  • Biochemistry/Molecular Biology: (BIOC/MICR 503/504)
  • Advanced Molecular Modeling: (MEDC 630/670)

Grant Funding

Cashman, D.J.; Baudry, J.B. Elucidation of the Protein-Protein Binding/Dynamics of Electron Transport Proteins with Cyanobacterial Photosystem I. TN-SCORE (Tennessee EPSCoR, NSF EPS-1004083). December 2014. $23,719 (TTU – Cashman) + $8,000 (UTK – Baudry) = $31,719. Funded.

Zhan, X. (PI); Cashman, D.J. (co-PI). Assembly, Dynamics and Allosteric Regulation of Arrestin-Mediated MAPK Cascades. National Science Foundation. Submitted: November 15, 2015. $395,637. Not Funded.

Renfro, M. (PI); Leckie, B. (co-PI); Hurt, C. (co-PI); Krosnick, S. (co-PI);Walker, D. (co-PI); Biernacki, J. (co-PI); Pascal, J. (co-PI); Zhang, L. (co-PI); Cashman, D.J. (co-PI); Datta, T. (co-PI); Kalyanapu, A. (co-PI); Ghafoor, S. (co-PI); Scott, S. (co-PI); Wolak, J. (co-PI); Cui, J. (co-PI); Languri, E. (co-PI); Shirvanian, A. (co-PI); Wilson, C. (co-PI); Holley, A. (co-PI); Kidd, M. (co-PI); Rajabali, M. (co-PI). HPC Computing Grant, Silicon Mechanics. Submitted: February 29, 2016. $100,000. Not Funded.

Zhan, X. (PI); Cashman, D.J. (co-PI). Assembly, Regulation and Catalysis of ASK1-initiated MAPK Cascades, National Science Foundation. Submitted November 15, 2016. $361,814. Not funded.

Cashman, D.J.; Callendar, A. The Science and Chemistry of Beer. EDGE Course Development Grant, Quality Enhancement Program (QEP), Tennessee Technological University. May 2018. $8,000. Funded.

Jiang, X.; Cashman, D.I.; Zhan, X. Redesign and Incorporation of 3D Modeling into Undergraduate Biochemistry Laboratory. EDGE Course Development Grant, Quality Enhancement Program (QEP), Tennessee Technological University, November 2019. $9100. Funded.

Renfro, M.; Hurt, C.; Cashman, D.J.; Vaselbehagh, A.; Eberle, W. Acquisition of a Next Generation High Performance Computing Cluster at Tennessee Tech. Major Research Infrastructure, National Science Foundation. Submitted January 2021. $988,702. Pending.Not Funded.

Adams, Allison and Cashman, D.J. Molecular Dynamics Validation of Computationally-Designed Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. Student Research Development Grant, Department of Chemistry, Tennessee Technological University. Fall 2021 – Spring 2022. Funded: $700.

Jiang, Xiaohua (PI); Lisic, E. (co-PI); Cashman, D.J. (co-PI); Zhan, X. (co-PI); Chitiyo, G. (Co-PI). Impact of Drug Discovery Research Experience on Minority Student Success. SERS, Tennessee Board of Regents. Spring 2022. $50,000. Not Funded.

Adams, Allison and Cashman, D.J. Computational Refinement of Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. Creative Inquiry Summer Experience (CISE) Grant, Tennessee Technological University. Summer 2022. Funded: $4,000.

Zhan, Xuanzhi (PI); Beck, D. (co-PI); Cashman, D.J. (co-PI). Developing Isoform-Specific Inhibitors of c-Jun N-terminal Kinase 3 With Therapeutic Potential for Neurodegenerative Diseases. Faculty Research Grant, Tennessee Technological University. Spring 2023. $20,000. Pending.

Publications

  1. Kellogg, G.E.; Scarsdale, J.N.; Cashman, D.J. (1999) Ligand Docking and Scoring in DNA Oligonucleotides. Binding of Doxorubicin and Modeled Analogs to Optimize Sequence Specificity. Medicinal Chemistry Research, Vol. 9, No. 7/8, 592 – 603.
  2. Cashman, D.J.; Rife, J.P.; Kellogg, G.E. (2001) Which Aminoglycoside Ring Is Most Important For Binding? A Hydropathic Analysis of Gentamicin, Paromomycin, and Analogues. Bioorganic & Medicinal Chemistry Letters, Vol. 11, 119 – 122.
  3. Cashman, D.J.; Scarsdale, J.N.; Kellogg, G.E. (2003) Hydropathic Analysis of the Free Energy Differences in Anthracycline Antibiotic Binding to DNA. Nucleic Acids Research, Vol. 31, No. 15, 4410 – 4416.
  4. Cashman, D.J. & Kellogg, G.E. (2004) A Computational Model for Anthracycline Antibiotic Binding to DNA: Tuning Groove-Binding Intercalators for Specific Sequences. Journal of Medicinal Chemistry, Vol. 47, 1360 – 1374.
  5. Cashman, D.J.; Rife, J.P.; Kellogg, G.E. (2004) Docking and Hydropathic Analysis of Hoechst 33258 with Double-Stranded RNA. Medicinal Chemistry Research, Vol. 12, No. 8, 445 – 455.
  6. Portugal, J.; Cashman, D.J.; Trent, J.O.; Ferrer-Miralles, N.; Przewloka, T.; Fokt, I.; Priebe, W.; Chaires, J.B. (2005) A New Bisintercalating Anthracycline with Picomolar DNA Binding Affinity. Journal of Medicinal Chemistry, Vol. 48, 8209 – 8219.
  7. Freyer, M.W.; Buscaglia, R.; Cashman, D.J.; Hyslop, S.; Wilson, W.D.; Chaires, J.B. Lewis, E.A. (2006) Binding of Netropsin to Several DNA Constructs: Evidence For at Least Two Different 1:1 Complexes Formed From an –AATT–containing ds–DNA Construct and a Single Minor Groove Binding Ligand. Biophysical Chemistry, Vol. 126, 186 – 196.
  8. Freyer, M.W.; Buscaglia, R.; Kaplan, K.; Cashman, D.J.; Hurley, L.H.; Lewis, E.A. (2007) Biophysical Studies of the c-MYC NHE-III1 Promoter: Model Quadruplex Interactions with a Cationic Porphyrin. Biophysical Journal, Vol. 92, 2007 – 2015.
  9. Cashman, D.J.; Freyer, M.W.; Dettler, J.M.; Hurley, L.H.; Lewis, E.A. (2008) Molecular Modeling and Biophysical Analysis of the c-MYC NHE-III1 Silencer Element. Journal of Molecular Modeling, Vol. 14, No. 2, 92 – 101.
  10. Mamonov, A.B.; Bhatt, D.; Cashman, D.J.; Ding, Y.; Zuckerman, D.M. (2009) General Library-Based Monte Carlo Technique Enables Rapid Equilibrium Sampling of a Protein Model with Atomistic Components. J. Phys. Chem. B, Vol. 113, No. 31, 10891 – 10904.
  11. Dettler, J.; Buscaglia, R.; Cui, J.-J.; Cashman, D.J.; Blynn, M.; Lewis, E.A. (2010) Biophysical Characterization of an Ensemble of Intramolecular i-Motifs Formed by the Human c-MYC NHE-III1 P1 Promoter Mutant Sequence, Biophysical Journal, 99(2), 561 – 567.
  12. Cashman, D.J.; Mamonov, A.B.; Bhatt, D.; Zuckerman, D.M. (2011) Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Using Well-Sampled Semi-Atomistic Monte Carlo Simulations. Current Topics in Medicinal Chemistry, Vol. 11, Issue 2, 211-220.
  13. Cashman, D.J.; Ortega, D.R.; Zhulin, I.B.; Baudry, J.Y. (2013) Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex. PLOS ONE, Vol. 8, Issue 8, e70705.
  14. Cashman, D.J.; Zhu, T.; Scott, C.; Bruce, B.; Baudry, J. (2014) Molecular Interactions Between Photosystem I and Ferredoxin: An Integrated Energy Frustration and Experimental Model. Journal of Molecular Recognition, Vol. 27, 597-608.
  15. 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.; Zaidi, S.A.; Kellogg, G.E. Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery, in Methods in Pharmacology and Toxicology (2015).
  16. Kapoor, K.; Cashman, D.J.; Nientimp, L.; Bruce, B.D.; Baudry, J. (2018) Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model. J. Phys. Chem. B, Vol. 122 (3), 1026 – 1036. Co-First Author *.
  17. Swartling, D.J.; Coonce, J.G.; Cashman, D. J. (2018) Using Balloons to Model Pi-Conjugated Systems and to Teach Frontier Molecular Orbital Theory. World Journal of Chemical Education, Vol. 6 (2), 102-106.
  18. Morris, W.H.; Ngo, L.; Wilson, J.T.; Medawala, W.; Brown, A.; Conner, J.D.; Fabunmi, F.; Cashman, D.J.; Lisic, E.C.; Yu, T.; Deweese, J.E.; Jiang, X. (2019) Structural and Metal Ion Effects on Human Topoisomerase IIα Inhibition by α-(N)-Heterocyclic Thiosemicarbazones. Chemical Research in Toxicology, Vol. 32 (1), 90-99.
  19. Hill, A.R.; Cashman, D.J.; Boles, J.O. (2020) Computational Analysis of Wild-type and Selenium-Incorporated Down-regulated Proteins in E. coli. The FASEB Journal, Vol. 34, Issue S1, 1-1.
  20. Zaharias, S.; Scull, N.; Zhang, Zihan; Davis, K.; Fargason, T.; Cashman, D.J.; Yu, T.; Lucius, A.; Zhang, J. Intrinsically disordered electronegative clusters improve protein stability and binding specificity of RNA-binding proteins. (2021) Journal of Chemical Biology, Vol. 297, Issue 2, 100945.
  21. Davis, C.W.; Pleinis, J.M.; Howlader, S.I.; Carter, K.N.; Trybala, T.N.; Cashman, D.J.; Zhan, X. Structural Basis of Docking Interactions among the Kinase Domains with ASK1-MKK-JNK3 Cascades. Manuscript in Preparation.
  22. Adams, A.G.; Cashman, D.J. In Silico Design of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. Manuscript in Preparation.

Presentations

  1. Cashman, D.J.; Kellogg, G.E. Docking and Scoring of Doxorubicin and 24 Analogs in DNA to Analyze Sequence Specificity. Sixteenth Annual Daniel T. Watts Symposium, Virginia Commonwealth University, Richmond, Virginia, November 1999. Poster
  2. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Docking and Scoring of Doxorubicin Analogs in DNA to Analyze Sequence Specificity. Virginia Meeting of the American Cancer Society, Norfolk, Virginia, March 2000. Oral
  3. Cashman, D.J.; Kellogg, G.E. Docking and Scoring of Doxorubicin and 40 Analogs in DNA to Analyze Sequence Specificity. School of Pharmacy Research Day, Virginia Commonwealth University, September 2000. Poster
  4. Cashman, D.J.; Kellogg, G.E.; Rife, J.P. Which Aminoglycoside Ring is Most Important to Binding? A Hydropathic Analysis of Gentamicin, Paromomycin, and Analogues. Seventeenth Annual Daniel T. Watts Symposium, Virginia Commonwealth University, Richmond, Virginia. October 2000. Poster
  5. Cashman, D.J.; Kellogg, G.E.; Rife, J.P. Determination of Hoechst 33258 Drug Binding Site in mRNA Using a Thermodynamic Molecular Probe. Eighteenth Annual Daniel T. Watts Symposium, Virginia Commonwealth University, Richmond, Virginia, October 2001. Poster
  6. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. The Hydropathic Analysis of DNA Intercalators to Design Highly Sequence-Specific Compounds. 80th Virginia Academy of Sciences Meeting, Hampton, Virginia, May 2002. Oral
  7. Cashman, D.J.; Kellogg, G.E. Scarsdale, J.N. Molecular Modeling of Doxorubicin Analogs with DNA Base Pair Quartet Sequences to Optimize Specificity. Bioinformatics & Pharmacogenomics 2002, Virginia Bioinformatics Consortium, Richmond, Virginia, June 12-14, 2002. Poster
  8. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Docking and Scoring of 60 Doxorubicin Analogs with 6 Unique DNA Base Pair Quartet Sequences to Optimize Sequence Specificity. Massey Cancer Center 2002 Research Retreat, Richmond, Virginia, June 14, 2002. Poster
  9. Cashman, D.J.; Kellogg, G.E. Scarsdale, J.N. Sequence Specificity Analysis of 60 Doxorubicin Analogs with 6 Unique DNA Sequences by Hydropathic Molecular Modeling Methods.” 224th ACS National Meeting, Boston, MA, August 18-22, 2002. Oral
  10. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Molecular Modeling Studies of 60 Doxorubicin Analogs in 6 Unique DNA Base Pair Quartet Sequences to Optimize Sequence Specificity. VCU Watts Day Symposium, October 2002. Poster
  11. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Molecular Modeling Studies of 60 Doxorubicin Analogs in 6 Unique DNA Base Pair Quartet Sequences to Optimize Sequence Specificity. VCU School of Pharmacy Research Day, November 2002. Poster
  12. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Determination of DNA Sequence Specificity of a Series of Doxorubicin Analogs Based on Hydropathic Molecular Modeling Studies.225th ACS National Meeting, New Orleans, LA, March 23-27, 2003. Oral
  13. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Determination of the Free Energy Differences in Anthracycline Antibiotic Binding to DNA by Hydropathic Methods. Graduate Research Association of Students in Pharmacy (GRASP) Conference, Virginia Commonwealth University, Richmond, VA, May 30 – June 2, 2003. Oral
  14. Cashman, D.J.; Chaires, J.B. Quantitative Analysis of Experimental Binding Affinities of 126 DNA-Binding Compounds verses 13 Nucleic Acid Sequences to Investigate Specificity. UT-ORNL Bioinformatics Summit 2005, Lake Barkley State Park, Cadiz, KY, April 1 – 3, 2005. Oral/Poster
  15. Cashman, D.J.; Lewis, E.A. Docking & Scoring of Netropsin to a DNA Duplex Structure. Annual UA-NAU Hurley Research Retreat, Carefree Resort & Villas, Carefree, AZ, February 25, 2006. Oral
  16. Cashman, D.J.; Lewis, E.A. Computational Analysis of the c-MYC NHE-III1 Silencer Element. Annual UA-NAU Hurley Research Retreat, Carefree Resort & Villas, Carefree, AZ, November 17-19, 2006. Oral
  17. Cashman, D.J.; Zuckerman, D.M. An Analysis of the Thermal Motions of Surface a-Helices in the E. coli D-Galactose Chemosensory Receptor using Coarse-Grained Monte Carlo Simulations. Third Annual Data & Dine Symposium, University of Pittsburgh Postdoctoral Association, University of Pittsburgh, Pittsburgh, PA. May 8, 2008. Poster
  18. Cashman, D.J.; Zuckerman, D.M. Insights into the Thermal Motions of the Glucose-Galactose Binding Protein in E. Coli Using a Semi-Atomistic Monte Carlo Simulation Method. Monthly Post-Doctoral Lunchtime Seminar Series. University of Pittsburgh Postdoctoral Association, University of Pittsburgh, Pittsburgh, PA. November 9, 2008. Oral
  19. Cashman, D.J.; Mamonov, A.B.; Bhatt, D.; Zuckerman, D.M. Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled “Semi-Atomistic” Simulations. 2009 Biophysical Society Meeting, Boston, Massachusetts. March 4, 2009. Oral
  20. Cashman, D.J.; Mamonov, A.B.; Bhatt, D.; Zuckerman, D.M. An Analysis of the Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Using a “Semi-Atomistic” Library-Based Monte Carlo Simulation Method. 2009 Fourth Annual Postdoctoral Data & Dine Symposium, University of Pittsburgh, Pittsburgh, Pennsylvania. May 19, 2009. Poster
  21. Cashman, D.J. Computational Simulations of Proteins Using a Fast, “Semi-Atomistic” Library-Based Monte Carlo Simulation Method. Department of Chemistry, Mississippi State University. March 12, 2010. Oral
  22. Collaco, A; Putzier, I.; Hong, L.; Chanthaphavong, S.; Lee, P.; Thickman, K.R.; Cashman, D.J.; Rajkumar, R.; Cronican, A.A.; Chuang, P.-Y.; Dagda, R.K.; Dudgeon, D.D.; Maul, T.M.; Woodcock, S.R.; Dennis, T.L.; Zellers, D.F. Postdoc Lunch Live! Providing a Monthly Forum for Postdoctoral Fellows to Develop Scientific Presentation Skills and Network with Colleagues Across the University of Pittsburgh. National Postdoctoral Association 2010 Annual Meeting, Philadelphia, Pennsylvania. March 12-14, 2010. Poster
  23. Cashman, D.J.; Ortega, D.R.; Zhulin, I.B.; Baudry, J.B. A Molecular Jigsaw Puzzle: Putting the Pieces of the Bacterial Chemotaxis System Together. Receptor Fest XIV. August 2, 2011, University of Utah, Salt Lake City, Utah. Oral
  24. Cashman, D.J.; Baudry, J.B. Conformational Analysis and Refinement of Homology Models of CheW Protein Using Molecular Dynamics and Monte Carlo Simulations. BCMB Symposium, University of Tennessee, Knoxville. September 20, 2011. Poster
  25. Cashman, D.J. Modeling of Proteins Involved in Bacterial Chemotaxis. BCMB Colloquium, University of Tennessee, Knoxville. October 3, 2011. Oral
  26. Scott, C.; Cashman, D.J.; Bruce, B.; Baudry, J.B. Modeling Protein/Protein Interactions: Three-dimensional Modeling of Psa C, D and E Interactions with Ferredoxin & Flavodoxin. BCMB Graduate Symposium, University of Tennessee, Knoxville. March 6, 2012. Poster
  27. Cashman, D.J.; Ortega, D.R.; Fleetwood, A.D.; Zhulin, I.B.; Baudry, J.B. Homology Modeling and Molecular Simulations of CheW. A Look into the Dynamic Nature of a Key Chemotaxis Protein. Computational Structural Biology 2012 Conference, UT/ORNL. June 3, 2012. Poster
  28. Cashman, D.J.; Ortega, D.R.; Fleetwood, A.D.; Zhulin, I.B.; Baudry, J.B. Studying the Structure and Dynamics of Bacterial Chemoreceptor Arrays Using Computational Methods. BCMB Day, University of Tennessee, Knoxville. September 4, 2012. Poster
  29. Cashman, D.J.; Ortega, D.R.; Zhulin, I.B.; Baudry, J.B. Studying the Protein-Protein Interactions of the Receptor Complex Involved in Bacterial Chemotaxis. UTK/ORNL Retreat 2013. March 1, 2013. Poster
  30. Williams, A.R.; Cashman, D.J. Applications of Computational Modeling Software for Use in the Instruction of General Chemistry. 9th Annual Student Research Day, Tennessee Technological University. April 10, 2014. Poster
  31. Oladinni, O.; Cashman, D.J.; Ballal, S.K. Computational Binding Site Analysis and Comparative Study of A, B and C RAF Kinase in bovine and pigs using an Integrated Energy Frustration Method. 2015 Southern Association of Agricultural Scientists Convention, Atlanta, Georgia. January 31 – February 3, 2015. Oral
  32. Cashman, D.J.; Oladinni, O.; Ballal, S.K. The Effects of Energetically Frustrated Residues on the Structural Dynamics of A, B and C RAF Kinases. 2015 Southern Association of Agricultural Scientists Convention, Atlanta, Georgia. January 31 – February 3, 2015. Oral
  33. Nientimp, L.; Baudry, J.; Cashman, D.J. Bioinformatics Methods Used to Probe the 3D Structure of Photosystem I. 10th Annual Student Research Day, Tennessee Technological University, Cookeville, Tennessee. April 9, 2015. Poster
  34. Nientimp, L.; Baudry, J.; Cashman, D.J. Probing the Potential Binding Sites of Cytochrome c6 and Ferredoxin with Photosystem I Using State-of-the-Art Bioinformatics Methods. TN-SCORE Annual Meeting, Nashville, Tennessee. June 18-19, 2015. Poster
  35. Cashman, D.J. Exploring the Protein-Protein Interactions and Structural Dynamics Between Cyanobacterial Photosystem I and Ferredoxin. Chemistry Department Seminar, Tennessee Technological University, Cookeville, Tennessee. September 25, 2015. Oral
  36. Cashman, D.J.; Kapoor, K.; Nientimp, L.; Baudry, J. Molecular Docking and Dynamics Studies of the Protein-Protein Interactions involved in Cyanobacterial Photosystem I and Ferredoxin, TN-SCORE Fall Research Meeting, Knoxville, Tennessee. October 12, 2015. Oral
  37. Cashman, D.J.; Kapoor, K.; Nientimp, L.; Baudry, J. Protein-Protein Docking and Molecular Dynamics Suggest Potential Mechanisms of Electron Transfer Between Ferredoxin and Cyanobacterial Photosystem I. Southeast Regional Meeting of the American Chemical Society, Memphis, Tennessee. November 4-7, 2015. Oral
  38. Andrews, Jen; Brookover, Zoe; Richard, Kaylie; Stark, Sophie; Subramanian, Deepak; Whitaker, Sydney; Nientimp, Luke C.; Cashman, D.J. 3D Models and Molecular Dynamics Used to Study Photosynthesis Proteins. 2015 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  39. Stout, R.; Cashman, D.J.; Zhan, X. Structural Basis of the Functional Differences Between Two Non-Visual Arrestin Isoforms. 11th Annual Student Research Day, Tennessee Technological University. April 6, 2016. Poster
  40. Jeskey, Alan; Kerns, Holli; Legaux, Nicholas; Seiber, Kristina; Vaughn, Vanessa; Yousef, Nassem; Williams, Adam; Cashman, D.J. Studying the MAPK Pathway and p38 Inhibitor Design Using Evolutionary Trace and Energetic Frustration Models. 2016 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  41. Mondal, J; Cashman, D.J.; Baudry, J.; Bruce, B.D. Engineering Enhanced Affinity Between Ferredoxin and Stromal Subunits of Photosystem I. 17th International Conference on Photosynthesis Research, Maastricht, The Netherlands. August 7-12, 2016. Poster
  42. Mohammad, A.S.; Biernacki, J.; Northrup, S.H.; Cashman, D.J. Molecular-Scale Modeling of Whole Biomass Pyrolysis – Morphological Changes. 2016 American Institute of Chemical Engineers Annual Meeting, San Francisco, California. November 13-18, 2016. Poster
  43. Mondal, J.; Cecil, J.; Cashman, D.J.; Baudry, J.; Bruce, B.D. Sticking it to PSI: Enhancing e- transfer thru T. elongates PSI by bioengineering the PSI:FD interface. The 26th Western Photosynthesis Conference, WPC/2017, San Francisco, California. January 5-8, 2017. Poster
  44. Suhagia, Tejaskumar; Cashman, D.J. QSAR Models of Organophosphate Pesticides. 12th Annual Student Research Day, Tennessee Technological University. April 6, 2017. Poster
  45. Fan, Rachel; Huynh, Brandon; Luthy, Claire; McNabb, Jackson; Pitts, Catherine; Zhou, Amy; Davis, Cameron; Cashman, D.J. Computational Drug Discovery of Novel Bacterial Dihydrofolate Reductase Inhibitors. 2017 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  46. Cashman, D.J.; Kapoor, K.; Nientimp, LC.; Baudry, J.; Bruce, B.D. Predictions of Protein-Protein Interactions and Conformational Dynamics of Cyanobacterial Ferredoxin and Cytochrome c6 with Photosystem I. The 27th Western Photosynthesis Conference, WPC/2019, Oracle, Arizona. January 5-8, 2018. Poster
  47. Mondal, J.; Cecil, J.; Cashman, D.J.; Baudry J.; Bruce, B.D. Sticking it to PSI: Enhancing e-transfer thru T. elongates PSI by Bioengineering the PSI:FD Interface. Predictions of Protein-Protein Interactions and Conformational Dynamics of Cyanobacterial Ferredoxin and Cytochrome c6 with Photosystem I. The 27th Western Photosynthesis Conference, WPC/2019, Oracle, Arizona. January 5-8, 2018. Poster
  48. Foster, S.T.; Cashman, D.J.; Ballal, S.K. Computational Predictions of the Binding Sites of RAF Kinases with h-RAS. 13th Annual Research and Creative Inquiry Day. April 9-10, 2018. Selected as Best Biology Poster
  49. Brown, Anna; Calhoun, Claire; He, Stephanie; Krishnan, Reethu; Stewart, Leon; White, Abbie; Dixon, Benjamin; Cashman, D.J. Computational Drug Discovery of M. Tuberculosis Tryptophan Synthase Inhibitors. 2018 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  50. Mondal, J.; Cecil, J.; Nguyen, T.; Kumar, R.; Cashman, D.J.; Bruce, B.D. Enhancing Electron Transfer Through Photosystem I (PSI) by Bioengineering the PSI-Ferredoxin Interface. The 28th Western Photosynthesis Conference, WPC/2019, Friday Harbor, Washington. January 4-7, 2019. Poster
  51. Burden, T.; Dixon, B.; Lyle, D.; Klingenberg, D.; Callender, A. Cashman, D.J. Barley: The Grain of the World. 14th Annual Student Research Day, Tennessee Technological University. April 8-9, 2019. Poster
  52. Vesely, J.; Reff, I.; Allen, J.; Winton, J.; Callender, A.; Cashman, D.J. It’s a Bine, Not a Vine – Literary Review of Hop Varieties. 14th Annual Student Research Day, Tennessee Technological University. April 8-9, 2019. Poster
  53. Gimicael, M.; Trotter, J.; Cai, E.; Marie, R.; Xian, K.; Chao, J.; Fabunmi, F.; Cashman, D.J.; Zhan, X. Biophysical Analysis of Protein-Protein Interactions of MAPK Kinase Signal Transduction Pathway. 2019 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Oral/Poster
  54. Hill, A.R.; Cashman, D.J.; Boles, J.O. Computational Analysis of Wild-type and Selenium-Incorporated Down-regulated Proteins in E. coli. 2020 National Meeting of the American Society of Biochemistry and Molecular Biology. April 1, 2020. Abstract Published in The FASEB Journal, Vol. 34, Issue S1, 1-1. Presentation canceled due to cancellation of national meeting resulting from the COVID-19 Pandemic.
  55. Dixit, M.; Marepally, H.; Mehta, K.; Seigler, C.; Tojaga, A.; Rogers, C.; Paris, R.; Cashman, D.J. Computational Drug Discovery of Novel Coronavirus Protease Inhibitors. 2020 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Virtual Oral/Poster
  56. Adams, A.; Cashman, D.J. Computational Design of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. 16th Annual Student Research Day, Tennessee Technological University. April 13, 2021. Poster
  57. Edmonds, M.; Carrick, Jesse D.; Cashman, D.J. Virtual Screening of Hamigomycin B Natural Product Derivativbes in 26 Kinase Proteins. 16th Annual Student Research Day, Tennessee Technological University. April 13, 2021. Poster
  58. Bays, J.; Bussa, V.; Jones, G.; Lawrence, G.; Liu, M.; McFadden, M.; McRae, J.; Mittal, M.; Moo, K.; Sathu, H.; Tian, A.P.; Zhang, E.Y.; Adams, A.G.; Cashman, D.J. Computational Drug Discovery of Novel Inhibitors of the COVID-19 Spike Protein. 2021 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Oral/Poster
  59. Davis, C.W.; Pleinis, J.M.; Howlader, M.S.I.; Carter, K.N.; Trybala, T.M.; Cashman, D.J.; Zhan, X. Structural Basis of Docking Interactions Among the Kinase Domains within ASK1-MKK-JNK3 Cascades. 131st Meeting of the Tennessee Academy of Sciences, Tennessee Technological University, Cookeville, TN. November 6, 2021. Oral
  60. Adams, A.G.; Cashman, D.J. Computational Design and Verification of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. 131st Meeting of the Tennessee Academy of Sciences, Tennessee Technological University, Cookeville, TN. November 6, 2021. Poster
  61. Edmonds, M.; Cashman, D.J.; Carrick, J.D. Computational Design  and Docking of Hamigeromycin B Natural Product Derivatives in 26 Human Kinases. 131st Meeting of the Tennessee Academy of Sciences, Tennessee Technological University, Cookeville, TN. November 6, 2021. Poster
  62. Adams, A.G.; Cashman, D.J. Computational Design and Molecular Dynamics Simulation of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. 17th Annual Research & Creative Inquiry Day. Tennessee Technological University. April 20-21, 2022. Poster
  63. Atkinson, Simone and Cashman, D.J.. Cross-Species Molecular Docking of Ferredoxin into Photosystem I of T. elongatus and Synechocystis sp. PCC 6803. 17th Annual Research & Creative Inquiry Day. Tennessee Technological University. April 20-21, 2022. Poster
  64. Edmonds, Meagan; Cashman, D.J. and Carrick, J.D. Computational Design and Docking of Hamigeromycin B Natural Product Derivatives in 26 Human Kinases. 17th Annual Research & Creative Inquiry Day. Tennessee Technological University. April 20-21, 2022. Poster
  65. Allison G. Adams and Cashman, D.J. Computational Analysis of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. 132nd Meeting of the Tennessee Academy of Sciences, Tennessee State University, Nashville, TN. November 18, 2022. Oral Presentation was awarded Best Undergraduate Presentation in Chemistry.
  66. Timothy C. Bryant; Zhan, X. and Cashman, D.J. The Structure of the N-Terminal Region of JNK3 and Its Binding Calculations With Upstream Kinases Using In Silico Prediction Methods. 132nd Meeting of the Tennessee Academy of Sciences, Tennessee State University, Nashville, TN. November 18, 2022. Oral
  67. Meagan Edmonds; Cashman, D.J. and Carrick, J.D. Computational Design and Docking of Hamigeromycin B Natural Product Derivatives in JNK3, EGFR, and Hsp90. 132nd Meeting of the Tennessee Academy of Sciences, Tennessee State University, Nashville, TN. November 18, 2022. Oral
  68. Trenton Martin; Zhan, X. and Cashman, D.J. Computational Docking of the N-Terminal Sequence of JNK3 and Arrestin-3. 132nd Meeting of the Tennessee Academy of Sciences, Tennessee State University, Nashville, TN. November 18, 2022. Poster
  69. Adams, A.G.; Cashman, D.J. Computational Design and Validation of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. Spring 2023 National Meeting of the American Chemical Society, Indianapolis, IN, March 25-30, 2023. Poster
  70. Edmonds, M.; Carrick, J.D.; Cashman, D.J. Virtual Screening of Hamigeromycin B Natural Product Derivatives in JNK3, EGFR, and Hsp90. Spring 2023 National Meeting of the American Chemical Society, Indianapolis, IN, March 25-30, 2023. Poster
  71. Davis, C.W.; Pleinis, J.M.; Howlader, S.I.; Carter, K.N.; Trybala, T.N.; Cashman, D.J.; Zhan, X. Structural Basis of Docking Interactions Among the Kinase Domains Within ASK1-MKK4-JNK3 Cascades. 13th Annual Southeast Enzyme Conference, Georgia State University, Atlanta, GA. April 22, 2023. Poster
  72. Anderson, N.; Kustoff, M.; Midgett, A.; Patri, A.; Waugh, C.; Nagy, H.P.; Cashman, D.J. Evaluation of Phosphoglucosamine Mutase AI Predictions as a Drug Target. 2023 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Oral

Students Mentored

A * indicates service as the student’s primary research advisor. A ** indicates service on the student’s graduate thesis committee.

  • Tyler McBride (UTK, undergraduate student); Fall 2012 – Spring 2013
  • Cathy Scott (UTK, MS graduate student); Spring 2012
  • Tuo Zhu (UTK, MS graduate student); Spring 2012 – Fall 2013
  • Adam Williams (TTU, undergraduate student); Fall 2013 – Spring 2014
  • Brita Anderson (TTU, MS graduate student); Fall 2013 – Summer 2015 **
  • Samar Aldhahry (TTU, MS graduate student); Fall 2013 – Spring 2016 **
  • Lasantha Rathnayake (TTU, Ph.D. graduate student); Fall 2013 – Summer 2017) **
  • Lola Oladinni (TTU, MS graduate student in Biology); Fall 2014 – Fall 2015 **
  • Luke Nientimp (TTU, undergraduate student); Fall 2014 – Fall 2015
  • Abdul S. Mohammad (TTU, MS graduate student); Spring 2016 – Fall 2016)
  • Qiao Chu (TTU, MS graduate student); Spring 2016 – Spring 2017 **
  • John Pleinis (TTU, MS graduate student, Spring 2016 – Fall 2016)
  • Nick Trybala (TTU, undergraduate student, Spring 2016 – Spring 2018)
  • Morgan Overstreet (TTU, undergraduate student, Summer 2017)
  • Cameron Davis (TTU, MS graduate student, Fall 2016 – Summer 2017)
  • Tejaskumar Suhagia (TTU, MS graduate student, Fall 2016 – Summer 2017 *
  • Adua Rahman (TTU, MS graduate student, Spring 2017 – Summer 2018) **
  • Rebecca Stout (TTU, MS graduate student, Spring 2017 – Summer 2018) **
  • Shanrya T. Powell (TTU, MS graduate student in Biology, Spring 2017 – Summer 2018) **
  • Amy Ridings (TTU, MS graduate student, Spring 2017 – Spring 2019) **
  • Florence Fabunmi (TTU, MS graduate student, Spring 2018 – Fall 2019) *
  • Sariful Howlader (TTU, MS graduate student, Fall 2017 – Summer 2019) **
  • Kristin Carter (TTU, MS graduate student, Fall 2018 – Spring 2020 **
  • Austin Hill (TTU, MS graduate student, Fall 2018 – Spring 2020) **
  • Allison Adams (TTU, undergraduate student, Fall 2020 – present)
  • Meagan Edmonds (TTU, undergraduate/graduate student, Fall 2020 – present) *
  • Amanuel Gimikael (TTU, undergraduate student, Fall 2020)
  • Hajar Taheri Afarani (TTU, Ph.D. graduate student, Spring 2021 – present) **
  • Jacob Thorn (TTU, MS graduate student, Spring 2021 – Fall 2022) **
  • Aaron Bain (TTU, Ph.D. graduate student, Spring 2021 – Spring 2022) **
  • Sekyere Boateng (TTU, MS graduate student, Spring 2021 – Summer 2022) **
  • Eric Agyei (TTU, MS graduate student, Spring 2022 – present) **
  • Simone Atkinson (TTU, undergraduate student, Fall 2021 – Fall 2022)
  • Timothy C. Bryant (TTU, graduate student, Fall 2021 – present) *
  • Ayessa Holbrook (TTU, undergraduate student, Summer 2022)
  • Victor C. Jonathan (TTU, MS graduate student, Fall 2022 – present) **
  • Miles Nevills (TTU, Ph.D. graduate student, Spring 2023 – present) **
  • Nathan Duran-Ledezma (TTU, Ph.D. graduate student, Fall 2023 – present)
  • Joshua Dean (TTU, undergraduate student, Fall 2023 – present)
  • Christian Scott (TTU, undergraduate student, Fall 2023 – present)
  • Muinat Zubair (TTU, MS graduate student, Spring 2024 – present)

Computer Experience

  • Highly skilled with several molecular modeling software packages, including MOE 2022, Chimera X, Gaussian 09, Tripos Sybyl, Accelrys Discovery Studio, VMD, InsightII, Cerius2, Hyperchem, PC SPARTAN, MacroModel, HINT (www.edusoft-lc.com), Unity, GRID, GAMESS, DOCK, Curves, and MDL QSAR.
  • Experienced with molecular dynamics software packages: AMBER, Gromacs, NAMD.
  • Experienced with High Performance Computing (HPC) clusters and supercomputing applications, MPI, SLURM, and multi-processor applications and simulations.
  • Experienced with programming in C/C++, Java, JavaScript, Fortran, Perl, PHP, MySQL, HTML, CSS.
  • Experienced with Mac OS X, Linux (OpenSuse, Red Hat, Ubuntu), and Microsoft Windows.
  • Experienced with Microsoft Office, ChemDraw, OpenOffice.org, Adobe Photoshop.

Awards & Recogniti0n

  • Region IV Distinguished Service Award; Alpha Phi Omega, December 2018. Awarded for outstanding community service on the regional level (Southeastern USA and Puerto Rico).
  • Best Practices in Teaching Certificate; University of Tennessee, Knoxville, December 2012.
  • Alpha Delta Iota (VCU) Chapter Distinguished Service Award; Alpha Phi Omega, November 2004. Awarded for outstanding community service at the local level.
  • Volunteer of the Year Award; FIRST (For Inspiration in Robotics, Science and Technology) Robotics Competition, March 2004.
  • Section 83 Distinguished Service Award; Alpha Phi Omega, March 2004. Awarded for outstanding community service at the sectional (Central & Eastern Virginia) level.
  • Outstanding Poster Presentation; VCU Watts Day Symposium, October, 2002
  • VCU Graduate School Travel Grant Award; 224th ACS National Meeting, Boston, MA, August, 2002
  • Outstanding Chemistry Presentation; 80th Virginia Academy of Sciences Meeting, Hampton, VA. May, 2002
  • Commonwealth Scholarship; VCU School of Pharmacy, 1999 – 2000
  • Student Leader Scholarship; Old Dominion University, 1993 – 1994

University Service Activities

  • Northrup / Clayton Molecular Modeling Laboratory; Coordinator (Fall 2015 – present)
  • Chemistry Department IT Committee (Fall 2014 – present)
  • Chemistry Department Graduate Recruitment & Admissions Committee (Spring 2023 – present)
  • Chemistry Marketing & Communications Committee (2016 – present)
  • TTU Food Science Working Group (2018 – 2020)

Academic & Community Activities

  • Alpha Phi Omega; Member of volunteer staff (since 1998). Advise and mentor students, present leadership workshops and seminars, and developed PHP/MySQL applications for the national website (www.apo.org). Currently serving as a Faculty/Staff Advisor to the Iota Alpha Chapter at the University of Tennessee – Knoxville (February 2012-present), as the Section 68 Chair for Eastern Tennessee (2012-2013), and as Section 70/I-2 Chair for Western Tennessee and Western Kentucky (2014-present).
  • American Society for Biochemistry and Molecular Biology; Serve as faculty advisor to the student affiliate chapter of the ASBMB at Tennessee Technological University. Fall 2013 -present.
  • American Chemical Society; Serve as a mentor to some students involved in the student affiliate chapter of the American Chemical Society at Tennessee Technological University. Fall 2013 – present.
  • Science Fair Judging; Served as a Judge for the Pittsburgh Regional Science and Engineering Fair (2009-2010), the Southern Appalachia Science and Engineering Fair (2012-2013), Tennessee Science Olympiad (2011 and 2012), and the Tennessee Chemistry Olympiad (2014-present).
  • University of Pittsburgh Postdoctoral Association; Marketing & Communications Officer (2008-2009). Responsible for organizing and promoting UPPDA events, including seminars, symposia, and other peer mentoring events. Maintained organization website, www.uppda.pitt.edu. Participation in events increased dramatically during my term of office.
  • Governor’s School for Emerging Technologies; (2015 – present) Serve as research mentor for teams of 6 – 12 high school students engaging in computational modeling projects to train them in STEM education.

Affiliations