Homology or comparative modeling is an efficient computational technique to generate the tertiary (3-D) structure of a protein from its amino acid sequence in cases where such structure has not previously been determined by experiment. The technique uses structural information for related proteins archived in the protein data bank (PDB) to predict the structure of the protein in question. Homology-based models can be used in several applications: for example, suggesting specific mutations that may influence the stability of function of the protein in particular ways. These models can also be used to study the conformational and dynamic properties of the protein, and to predict interactions with other proteins, nucleic acids or drug molecules. Homology modeling can, therefore, fill in the gaps in our knowledge of protein structures that have not been or cannot be solved by experimental methods such as X-ray diffraction and nuclear magnetic resonance (NMR).
The CCB offers expertise in a wide range of computational, structural-biological applications, such as:
- Prediction of 3-D protein structure from sequence data using homology modeling techniques.
- Prediction of the effects of amino acid changes on protein stability and function.
- Prediction of functional residues in a protein from sequence and structural information.
- Analysis of electrostatic and dynamic properties of proteins using state-of-the-art molecular dynamics simulation methods and electrostatics calculations.
