RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps

The Structure Superposition Database

The need for new tools for investigating biological systems on a large scale is becoming acute, particularly with respect to computationally intensive analyses such as comparisons of many three-dimensional protein structures. Structure superposition is a valuable approach for understanding evolutionary relationships and for the prediction of function. But while available tools are adequate for ...

Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures

Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure cha...

structureViz: linking Cytoscape and UCSF Chimera

structureViz is a Cytoscape plug-in that links the visualization of biological networks provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera. When combined with Cytoscape and Chimera, structureViz provides the first tool that links these two critical aspects of computational analysis in a straightforward manner. structureV...

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures

SUMMARY LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biol...

Homology Modeling in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction) Using CHIMERA and FAMS