Computational Chemistry Shared Resource – Services

Contact Information

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

CCSR Services

CCSR provides a range of support services including new small molecule screening & discovery, drug repurposing, chemo-and pharmaco-informatics, systems pharmacology, and molecular modeling services listed below.

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.

  • Integrated systems pharmacology and cellular network analysis.