Computational Chemistry Shared Resource (CCSR)

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.