NYMC > Research > Core Facilities & Shared Resources > Molecular Modeling

Molecular Modeling

The Department of Biochemistry and Molecular Biology houses a high resolution molecular modeling computer workstation essential for three-dimensional structure analysis of biological micro- and macro-molecules. It provides a complete simulation environment in which molecular models can be created, viewed and analyzed. Computer aided molecular design enables simulation of the structure, behavior and interaction of molecules on computers and allows visualization of dynamic changes in structures.

The facility comprises a Silicon Graphics 6000 octane graphics workstation and uses the Insight II 3-D graphics program, an extensive suite of modeling tools to create, modify, manipulate, display and analyze molecular systems and related data. This integrated approach facilitates rapid verification of simulated data against experimental data. The complete molecular modeling environment allows the researcher to:

Construct models of peptides, proteins, carbohydrates and nucleic acids for visualizing complex macromolecular structure.

Build a 3-D model of protein from its amino acid sequence and the known structure of related proteins using standard techniques of backbone building, loop modeling, structural overlay and statistical analysis of the resulting models.

Generate automatically a refined homology model of a protein, given only the sequence alignment to a known 3-D protein structure, and enabling generation of excellent structural models with as little as 30 percent homology to known structures.

Incorporate a range of well validated force fields for dynamic simulation, minimization and conformational searches, allowing prediction of the structure, energetics and properties of macromolocules of biological interest.


Department of Biochemistry and Molecular Biology
Basic Sciences Building
Valhalla, NY 10595
Tel: 914/594-4055
Fax: 914/594-4058