Computational Chemistry & Biology Services

Computational chemistry, computational biology services

  • For nonprofit, academic, and industrial researchers involved in drug discovery and development

  • Access to cutting-edge computational tools and resources

  • No need to invest in software, hardware, or a comp chem FTE
  • Access to commercial and proprietary software (solvation free energies of waters; distinctive PPI applications)
  • All tools web enabled so work can be completed at the client's site

  • We help increase your success in:

  • Hit identification, lead qualification and lead optimization
  • Accelerating medicinal chemistry projects
  • Likelihood of grant renewals, attracting investment funding, or licensing/collaboration opportunities

  • We are fully committed to the success of your discovery projects

  • To add value in a variety of ways

  • Hit/Lead Optimization

    Molecular Dynamics

    Molecular dynamics simulations

    Complementarity of ligand flexibility and protein flexibility

  • e.g. ligand causing loop movement, binding stability, etc.

  • Quantum Mechanical Dynamics

    Quantum mechanical simulations

    Charge sharing between ligand and biomolecule as it impacts binding

  • Quasi-covalent binding, site-specific partial charges

  • Quantum Mechanical Dynamics

    Hot-spot mapping*

    Locating novel pockets/sub-pockets of high interaction energy, druggability

    *"Diverse Fragment Clustering and Water Exclusion Identify Protein Hot Spots" Kulp et al. JACS 2011 133(28), 10740-10743.

    Quantum Mechanical Dynamics

    Water mapping**

    Estimate of binding affinity (free energy) and rank-ordering

  • Determines the ligand’s ability to dislodge, preserve, or interact with specific waters
  • Accurate predictions based on annealing of chemical potential in a Grand Canonical Monte Carlo simulation

    **“A fragment-based approach to the SAMPL3 Challenge” Kulp at al. J Comput. Aided Mol Des. 2012 26(5), 583-94.

    Computational Chemistry Services

    Ligand-based Drug Design

    • QSAR, shape-based screening, core hopping, analog-by-catalog similarity searches, conformational analysis

    Structure-based Drug Design

    • Homology modeling, docking (induced-fit, covalent, QM-polarized), fragment-based ligand growth and optimization

    In silico ADME

    • Rapid predictions of pharmaceutically relevant properties

    Compound libraries

    • Commercially-available libraries for virtual screening
      • ZINC (~35 million compounds)
      • Emolecules (~6 million compounds)
    • Exclusive libraries for virtual and experimental screening
      • Blumberg Institute’s 85,000 compound library
      • Pennsylvania Drug Discovery Institute’s 10,000 compound/reagent library