title: Interactive modeling of supramolecular assemblies.
abstract: The modeling of supramolecular structure presents two major challenges: (1) managing the large amount of sequence, structural and biochemical data, and (2) presenting the data to the user in a flexible and comprehensible manner that addresses these problems. We describe a visualization environment for the creation and analysis of supramolecular models. A set of modular symmetry tools, collectively called SymGen, has been created, providing a flexible platform for the creation of complex assemblies, with interactive control of all symmetry elements and their parameters. A second tool, SymSearch, allows a range of parameters defined within SymGen to be sampled and the resulting conformations to be evaluated. The environment avoids information overload, caused by the large number of atoms in supramolecular complexes, by using a multiresolution spherical harmonic representation that allows the user to display only essential features. Spherical harmonics also enables control of the triangulation level, allowing the user to reduce the complexity of the geometric description to retain interactive speed. The visual fidelity of the surface data is retained by using texture maps that are independent of the resolution of the underlying triangulation. We describe the design and implementation of this environment, and three illustrative examples of its utility.
authors.affiliation: Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: T J
authors.initials: TJ
authors.lastname: Macke
authors.forename: B S
authors.initials: BS
authors.lastname: Duncan
authors.forename: D S
authors.initials: DS
authors.lastname: Goodsell
authors.forename: A J
authors.initials: AJ
authors.lastname: Olson
mesh_terms: D002213:Capsid / Q000737:chemistry; D003198:Computer Simulation; D018031:Connexin 43 / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D017955:Poliovirus / Q000737:chemistry; D011487:Protein Conformation; D012984:Software
chemical_list: D018031:Connexin 43