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Molecular Modeling Laboratory for Cancer Therapeutics

The BCCC-CURE Molecular Modeling Laboratory for Cancer Therapeutics is a shared resource for BCCC-CURE researchers and graduate and undergraduate students to learn about and apply computational modeling tools to their cancer research projects in an interdisciplinary environment.

Bioinformatics and structure-based computer modeling tools have contributed to the discovery of many cancer drugs on the market, and new waves of advanced computational models are revolutionizing computer-aided drug discovery programs in academia and industry. Modern drug-discovery modeling software tools often require specialized expertise and dedicated high-performance computer hardware resources not often available in medicinal chemistry laboratories. The BCCC-CURE Molecular Modeling Laboratory fills this need by providing a space as well as physical and intellectual resources to deploy advanced computer modeling research techniques to find new cancer therapies.

The BCCC-CURE Molecular Modeling Laboratory for Cancer Therapeutics is co-directed by Prof. Shaneen Singh (Biology) and Prof. Emilio Gallicchio (Chemistry).

S.SinghProf. Shaneen Singh
A novel feature of our approach is the integration of bioinformatics tools to analyze genomic and proteomic data with detailed computational analysis of the physical interactions…[read more]

PEmilio Gallicchiorof. Emilio Gallicchio
The overall aim of the research is to deploy sophisticated molecular theories, efficient algorithms, and powerful computers to characterize fundamental chemical and biological mechanisms…[read more]

Ongoing Interdisciplinary Projects:

  • Conformational propensities and tubulin binding of colchicine analogs (Murelli, John-Charles Baucom, Gallicchio)
  • Optimization of stapled peptides (Gerona-Navarro, Katherine Menendez, Gallicchio)
  • Untangling the Interconnected Roles of Nucleolin and BRCA1 in Breast Cancer (Saxena, Singh)


  • Schrodinger Small-Molecule Drug Discovery Suite: Ligprep (drug protonation/tautomerization), Glide (docking), Prime (protein structure prediction), Jaguar (electronic structure), Desmond (molecular dynamics)
  • AToM-OpenMM: absolute and relative binding free energy calculations.
  • Open source/web based molecular modeling tools (Modeller, Robetta, I-Tasser, Alphafold, Quark, SwissModel, Model evaluation web servers)
  • Visualization and biophysical analysis software (Pymol, Cn3D, VMD, Chimera)
  • Docking and analysis software( Autodock, ADT tools, HDock, Cluspro, Haddock, PDBsum, Ligplot)


  • Computational molecular biophysics laboratory 3316 Ingersoll: 9 research workstations and computational servers, 24 GPU accelerators.
  • Bioinformatics laboratory 217 New Ingersoll: 6 Imac Workstations.