Available Software Packages
The facility offers access to state a variety of software packages for structure visualization, modeling and analysis. Researchers are trained in software tools for protein and DNA sequence analysis, protein fold determination, structure superimposition and comparison, homology modeling, active site identification, mutation effects analysis, and drug docking. Available software packages include SYBYL, Insight II, FELIX, QUANTA, spock, VMD, CCP4, AMBER, FlexiDock, and many others. In addition, programs are available for structure determination using X-ray crystallography or NMR spectroscopy.
Sequence Analysis
Multiple sequence alignments, phylogenetic analysis, ancestral sequence predictions, secondary structure predictions, domain prediction, functional residue prediction
Structure Visualization and Analysis
Structure visualization, electrostatic surfaces, homology modeling, amino acid mutation analysis, solvent accessibility calculations, subunit contact analysis, molecular dynamics calculations, free energies of binding, active side identification, docking of small molecules, figures for grants and publications, molecular movies for presentations
X-ray Crystallography
Data reduction, molecular replacement, density modification, model building, model refinement