Technology


integrated computational and experimental fragment-based platform

Conifer Point’s integrated computational and experimental fragment-based platform creates a map of where, and with what affinity, fragments bind to the target protein. Using structure-based design, our chemists turn hits into leads efficiently, thus saving time and money.

Publications

  • "Diverse Fragment Clustering and Water Exclusion Identify Protein Hot Spots" Kulp et al. J. Am. Chem. Soc. 2011 133(28), 10740-10743.
  • “A fragment-based approach to the SAMPL3 Challenge” Kulp at al. J Comput. Aided Mol Des. 2012 26(5), 583-94.

Software

Custom Fragment-based Design Software (unique to our services)

  • Grand canonical Monte Carlo molecular simulator
  • Fragment-based design tool platform for visualization, search, and ligand binding evaluation

Commercial and academic software

  • GAMESS for quantum mechanical simulations supported by a custom Web front-end for fragment, ligand, and protein residue partial charge calculations
  • GROMACS for molecular dynamics simulations and AutoDock Vina for ligand docking
  • ChemBioOffice for documentation and SciFinder for compound, reaction, and patent research
  • Other commercial software also available

Equipment

In house

  • >1,000 ft2 combined lab and office infrastructure
  • Analytical Agilent 1100 HPLC
  • Agilent LC-MS (1200)
  • Shimadzu Preparative HPLC
  • Parr hydrogenator with heating capability
  • Radley's carousal unit for parallel synthesis
  • Teledyne/ISCO CombiFlash Companion Flash Chromatography System (3)
  • Rotavapor (3)
  • Large scale reactors, 5L-50L
  • Low bench hood for large scale synthesis

Shared with other companies at the center or through collaboration

  • MALDI and Thermo Finnigan LCQ-Ion trap
  • Varian Mercury Plus 300-MHz Inova NMRs with multinuclear capability (1H, 13C, 31P, 18F)
  • BSL-2 and BSL-3 biological labs and tissue culture labs
  • Biacore surface plasmon resonance T200

Computing Resources

  • An internal cluster of 144 cores and > 30TB storage
  • Dell Precision dual-processor Xeon 5680 workstations with Nvidia 470GTX graphics cards
  • Cloud computing (Amazon EC2) for large scale simulations and on-demand data delivery

Screening Libraries

  • Full Access to Baruch S. Blumberg Institute’s 85,000 compound library (onsite)
  • Full Access to Pennsylvania Drug Discovery Institute resources (onsite):
    • Reagent Collection: >10,000 reagents, bar coded, searchable database