Background


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RD Clark

  
Dr. Clark was born and raised in southwestern Michigan. After pursuing undergraduate studies in chemistry, mathematics and Russian at Deep Springs College and Ohio University, he went on to do graduate work in biochemistry, statistics and biometry at Cornell University, receiving his PhD at the end of 1981. 

After spending two years of post-doctoral work at Brookhaven National Labs, he moved to St. Louis to work at Monsanto Agricultural Co. on molecular design, physiology, screening, and SAR-guided pesticide synthesis. Tripos lured him away in 1994 to put his experience to work in expanding the range of software available to help others working in similar areas.  Bob eventually became Vice President of Science and Research at Tripos, which he left to found his own research and consulting company, Biochemical Infometrics.  He was hired as Director of Life Sciences at Simulations Plus in January 2010, and became a Sr. Research Fellow in 2018. He became an Emeritus Fellow in 2021.

Bob became fully retired in 2022 but continues as an adjunct professorship in the School of Informatics at Indiana University, a position he has held since 2006. Biochemical Infometrics is being resurrected as a one-man non-profit consulting operation - for a while, at least.  

The broad range of technical journals for which he reviews manuscripts - the Journal of Medicinal Chemistry, the Journal of Agricultural and Food Chemistry, Pest Management Science, the Journal of Chemical Information and Modeling, and the Journal of Computer-Aided Molecular Design, among others - attests to the breadth of his expertise and experience.

Professional Experience

  • Indiana University, Bloomington (Jan 2006-present)

Founder and Chief Scientist.

Research and consulting company launched in mid-2008 to encourage the development, characterization and careful application of molecular design methods.

Director, Life Sciences; Director, Cheminformatics; Sr. Research Fellow; Emeritus Fellow.

Notable personal accomplishments include the discovery that beta binomial and gamma distributions can be used to estimate uncertainties for individual predictions derived from ensemble classification and regression QSAR models, respectively. Oversaw the merger of ADMET Predictor and MedChem Studio into a single product with a unified code base. Led research teams devoted to the R&D behind GastroPlus and  MembranePlus as well MedChem Studio and ADMET Predictor when they were individual products.

Sr. Scientist; Director of Research; VP of Science & Research.
      Led the Informatics Research Center, which was responsible for finding new computational methods to aid the discovery and development of biologically active small molecules and for determining how such methods can be best applied. I was responsible for overall IP strategy, promoting scientific innovation, ensuring the scientific soundness of the company as a whole, and managing academic and industrial research collaborations. Areas of concentration have included HTS data analysis, lead optimization, in silico ADME/Tox and drug design in general.
Developed isotropic field orientation for CoMFA clustering (IFO-COMFA) and ensemble modelling for HQSAR.  Invented the optimizable K-dissimilarity selection method (OptiSim) used in subset selection, fingerprint visualization (HTS DataMiner), combinatorial docking (OptiDock), combinatorial library design (OptDesign), and other Tripos tools. Co-inventor of topomers and CHEMSPACE.  Invented the GALAHAD technology used for ligand alignment and pharmacophore elucidation.
  • Agricultural Group of Monsanto Company (July 1984 - June 1994)
Research Specialist; Research Chemist; Herbicide Early Evaluation Team Leader; Sr. Research Chemist.

Elucidated mode(s)-of-action of herbicides by carrying out complementary biochemical and physiological studies of herbicide mode-of-action and metabolism, directing synthetic efforts towards increased potency and selectivity.

Delineated the role of the peroxide burst in soybean resistance to Phytophthora zoospores and its involvement in wheat "resistance" to transformation by Agrobacterium.  Helped develop the dot-blot assay for neomycin phosphotransferase (NPT II) now widely used to assess plant transformation.

Responsible for test design and evaluation in primary and secondary greenhouse testing, interfacing with Discovery, Synthesis and Advanced Biology teams. Integrated modelling and experimental design into primary and secondary herbicide evaluations.

Initiated combinatorial synthesis program for fungicide lead follow-up after having created two new herbicide classes, including the company's first chiral field candidate.  Responsible for design and synthesis of new herbicides for use in European small grains, and for successfully improving toxicological and environmental profiles by application of biorational principles.

Education

  • Post-doctoral Training: Biology Department, Brookhaven National Laboratory (1/82-6/84)
Worked as a post-doctoral student in Geoffrey Hind’s laboratory to isolate and characterize cytochrome b6f complex from spinach and to study its interaction with the light harvesting chlorophyll ab binding protein kinase (LHCK) in spinach.  This work is still relevant to research being carried on 20 years later (Mullineaux & Emlyn-Jones, J. Exp. Biol. 2005, 56, 389-393).
  • Ph.D.: Cornell University; NSF Graduate Fellow in Biochemistry, Molecular & Cell Biology.
Doctoral Thesis (1981): "Energy Transduction in Halobacterium halobium." Studied under Russell MacDonald.  Demonstrated light-driven ATP synthesis coupled to halorhodopsin turnover both in vivo and in vitro.  The latter involved isolating membrane vesicles from mutant cells, loading them with ADP and phosphate by osmotic shock, then measuring light-induced synthesis of ATP inside the vesicles. Minored in statistics and biometry.
  • M.S.: Chemistry, Ohio University, Athens OH (7/76-9/77) under John Blazyk. 
Studied the kinetics of NADH:NADP transhydrogenase in submitochondrial particles from bovine heart via UV/VIS spectroscopy using an array of spectrally distinct substrate analogs.
  • B.S.:  summa cum laude in Chemistry, Honors Tutorial College, Ohio University (9/74-6/76).  

  • Attended Deep Springs College, Deep Springs CA (7/73-6/74).