Question 1

General capabilities

Accepted Answer

High quality graphics with advanced display options and stereo support
Ability to generate publication quality images
Interactive 3D graphical view with associated hierarchy and data table views
Multiple sided surfaces and isosurfaces for enhanced molecular visualization
Ability to plot data from multiple data series with line and point plots, 3D plots and bar charts
Charting capability including heat maps, histograms, hit rate plots and more
Storyboard functionality to capture series of molecular views to demonstrate and share
Export storyboards as movies
Sorting, filtering and grouping functionality available for properties in the data table
Perl scripting to automate repetitive tasks or link tasks together for ease of use
Tool panels, tool bars and interface layout can be customized as desired
Support for a wide variety of structure and sequence file formats
RMS calculations available at different levels of detail
Monitors available for a wide variety of favorable, unfavorable and unsatisfied non-bond interactions

Question 2

Protein design and visualization

Accepted Answer

Molecular Builders for peptides and nucleic acids
Calculation of Solvent Accessibility to identify buried and exposed residues
Graphing functionality, including Ramachandran and contact plots
Load protein structures directly from the PDB database
Generate protein reports to summarize data in protein structures
Construct the biologically active unit of a protein from its subunits
Clean protein functionality to add missing side-chains, remove disorder and standardize atom naming
Enhanced display of protein and nucleic acid sequences and analysis of their composition and alignments
Superimpose structures based on tethers, residues and sequence alignment
Secondary structure prediction of protein sequences
Annotation window to view and edit annotations for nucleic acid and protein sequences
Display and contour X-ray electron density maps
Basic tools to edit X-ray structures
Sampling of side-chain rotamer conformations and interaction analysis

Question 3

Ligand design and visualization

Accepted Answer

Receptor-ligand interaction surfaces displaying hydrophobicity, hydrogen bonding, aromaticity and more
View 2D depiction of molecules in the data table
Sketching tools to create new small molecules
Modify or build custom 3D small molecules using a tool panel of pre-defined fragments
Optimize the geometry of built structures with a fast Dreiding-like forcefield
Basic molecular properties can be calculated such as molecular formula and molecular weight
Superimpose structures based on molecular overlay using field alignment or tethers
Define, display and edit ligand binding sites
Generate 2D receptor-ligand interaction plots
Analyze the ligand binding patterns between a protein and its bound ligands
Manually generate pharmacophore (Catalyst) queries

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