Tools for integrated sequence-structure analysis with UCSF Chimera

The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided.The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is available for Microsoft Windows, Apple Mac OS X, Linux, and other platforms from http://www.cgl.ucsf.edu/chimera webcite.Integration of protein sequence and structure information is essential in many problem domains, including structural biology, protein engineering, and drug design. A suite of tools within UCSF Chimera [1] has been developed for studying sequence-structure relationships and comparing related structures.Common tasks in sequence-structure work include: (A) displaying information from a sequence alignment on one or more corresponding structures, or displaying information from the structures on the alignment; (B) superimposing structures so that they can be compared; (C) generating a structure-based sequence alignment.The Multalign Viewer extension of Chimera displays sequence alignments and automatically associates structures with sequences in the alignment. Structures can be superimposed using the alignment, and sequence-related data such as conser