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The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who(More)
BACKGROUND Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond(More)
We have implemented extensions to the Brookhaven Protein Data Bank (PDB) file format for incorporating scene information such as viewing parameters, additional molecular information (e.g., van der Waals radii and atom colors), and user-defined graphics. These extensions were made in conformance with the PDB standard and provide sufficient information to(More)
With the increase in the number of large, 3D, high-resolution nucleic acid structures, particularly of the 30S and 50S ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. Large molecular structures are complicated and detailed, and one goal of visualization software is to(More)
We describe the Object Technology Framework (OTF) software system developed at the University of California, San Francisco Computer Graphics Laboratory for creating C+2 classes that facilitate rapid biomolecular application development and the application of the OTF to collagen modeling. C+2 class libraries for accessing and manipulating data from standard(More)
Proteins are the building blocks of life. Conserved protein sequence patterns called " motifs " and " domains " are well-known to be associated with protein function and biological activity. Growing biological and bioinformatical information for protein families already exists in free online databases like PFAM [2]. In collaboration with the University of(More)
MidasPlus [6, 7] is an interactive molecular modeling system used to depict three dimensional macromolecular structures such as proteins and nucleic acids, to study how these structures spatially and chemically interact, and to study how small molecules such as drugs bind with these macromolecules, Effective interaction with macromolecular structures(More)
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