Visualization of Biomolecular Complexes Vijay Reddy The Scripps
Visualization of Bio-molecular Complexes Vijay Reddy The Scripps Research Institute
Visualization gets the attention: A picture is worth a 1000 words & x 106 coordinates • Crucial for understanding a system (quickly) • Concise/faster way of representing large amount of data • Research tool: Aids in the molecular design and analyses • Educational tool: A video keeps the kids still and gets their attention.
Viral capsids represent the biggest macromolecular complex structures determined # atoms ~64, 000 ~3, 500, 000 (Tex. Mol representations at http: //viperdb. scripps. edu)
http: //viperdb. scripps. edu
http: //viperdb. scripps. edu/info_page. php? VDB=1 w 8 x
http: //viperdb. scripps. edu/info_page. php? VDB=1 w 8 x
Gallery of big virus capsids in VIPERdb PBCV-1 Virus Capsid, 1 m 4 x, Chlorovirus, Phycodnaviridae
Visualization wish list of Structural Virologists • Represent x 106 of atoms – Handle different types of residues: proteins, nucleic acids carbohydrates, lipids, hetero atoms • Impose symmetry – NCS as well as Crystal symmetries • Stereo chemistry auto check/ Feed back/ Validation • Compare with known/similar (b. b, s. c. ) conformations in PDB • Display electron densities on larger grids (1000 x 1000) = 10 9 grid points • Multi-resolution visualization – Back and forth between fine and coarse grids • Interactive: rotate/translate/zoom/slice/dice – map chosen properties (e. g. , B-factors, SASA) on to models and maps • Real space refinement (ability to interface with other programs) • Platform/OS independent • Ability to interface with the WWW in terms of plugins (e. g. , vrml, xvrml).
- Slides: 8