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.