Tools for integrated sequence-structure analysis with UCSF Chimera

By Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, Conrad C. Huang, T. Ferrin. BMC Bioinformatics, 2006

704 citations recorded by the source corpus.

BackgroundComparing 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 mapping where a sequence region falls in the structure and vice versa; (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit); (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals.ResultsThe 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.ConclusionThe 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.

Subfields: Biomedical Engineering, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8a7be50a5e678a67922884290f9a09deb15ab8e4

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biomedical Engineering

In Materials Chemistry

In Molecular Biology

Citations in the corpus

MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation (2020, methodology): “Structure and amino acid sequence analyses and representation Structures were superimposed using Chimera MatchMaker [91].”
UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “These capabilities augment over 100 tools already provided by Chimera for the interactive analysis of atomic models, density maps, and protein sequences (Couch et al., 2006; Goddard et al., 2005, 2007; Meng et al., 2006; Morris et al., 2007; Pettersen et al., 2004; Pintilie et al., 2010).”
Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies (2009, neutral): “Align commands[42].”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, methodology): “UCSF Chimera is a graphics program for analysis and interactive visualization of molecular structures and related data (40).”