Computational Chemistry Shared Resource (CCSR)

Contact Information

Sivanesan Dakshanamurthy, PhD, MBA
Director of CCSR
Telephone: (202) 687-2347
Office: New Research Building E401

CCSR Services

Services offered by the Computational Chemistry Shared Resource include:

  • Research and development to fit users’ specific drug discovery, molecular modeling and computational chemistry project needs
  • Advice and guidance on the use and applications of methodologies to support the experimental design
  • Support for the writing of properly powered computational modeling and drug discovery grant proposals and scientific manuscripts
  • Mentoring of staff, technicians and students involved in projects
  • Training on the safe and proper use of instrumentation

Research Support offered by the Computational Chemistry Shared Resource include:

  • Small molecule virtual screening: A major goal of the CCSR is to aid in the discovery and design of novel small molecule drugs by rapidly identifying and refining promising compounds utilizing a variety of strategies, including:
    • Structure based virtual high-throughput screening of small molecules to identify potential lead compounds
    • Drug repurposing screens
    • Lead modification of small molecule scaffolds to optimize potency and specificity
  • Molecular modeling and analysis:  Determining the structure and properties of biomolecules for understanding the fundamentals of protein-protein interactions, and small molecule design.
  • Protein sequence analysis and 3D structure predictions: Protein-ligand, and protein-protein interactions, protein-antibody, antigen-antibody docking
  • Biomolecule simulations: The CCSR performs sophisticated simulations of the potential interactions between macromolecules, ligands, membrane surfaces, and metal ions using molecular mechanics, quantum mechanics, molecular dynamics calculations. Capabilities include:
    • Prediction of dynamicity of proteins using molecular dynamics simulations
    • Optimization and minimization of proteins, and other biomolecules using Molecular mechanics simulations
    • Predicting effects of amino acid mutations or modifications on properties such as structural alterations, protein folding & stability, binding affinity
  • Chemo-informatics services: The cheminformatics service supports compound management, SAR analysis, and data simulations. The 2D and 3D SAR results can be further utilized in small-molecule design for custom synthesis or commercial acquisition of follow-up compounds. Services include:
    • Generation and validation of qualitative and quantitative ligand based pharmacophore models to identify more potent candidates.
    • Ligand structure based virtual screening to identity potent small molecules
    • Generation of quantitative structure activity relationships (2D-3D QSAR) lead candidates
    • Design of follow-up compounds or libraries
    • Prediction of ADME-Tox properties
  • Systems Pharmacology/Network Services: We provide support that integrates computational chemistry data simulations with network biology/medicine data. This includes integrated systems pharmacology and cellular network analysis.