Molecules to maps: tools for visualization and interaction in computational biology

Tools for visualization and interaction in computational biology attempt to assist scientists in understanding and correlating the often vast quantities of data produced both by direct observation of biological samples and as a result of further analysis or correlation of such data. Other tools and techniques are being developed to assist scientists in presenting their results to others in richer, more meaningful formats. This conference track explores novel tools and techniques in visualization and interaction to support scientists in exploring, navigating, and evaluating this data, and tools that assist scientists in presenting their results in a format that takes advantage of the latest advances in publishing technology, exploiting characteristics of human perception to effectively convey information to viewers. The Chimera molecular modeling system, rst presented at PSB '96, is an extensible molecular modeling application constructed using standard components. Two papers in this track present extensions to Chimera. Huang, et al describe three new computational methods, each with an associated visual interface, designed to assist scientists in the integration of sequence and structure. MinRMS generates a family of structural alignments based on optimal RMSD (root mean square distance) superpositions of alpha-carbon atoms in the structures being compared. AlignPlot provides a graphical representation of the RMSD values for each alignment in a set, allowing users to quickly identify areas of structures that are most similar and serving as a navigation tool between alignments. MSFViewer displays multiple alignments of related sequences and supports interactive highlighting of alignments. Overall, the goal of this work is to provide a comprehensive set of tools for generating and testing hypotheses about sequence, structure, and functional relationships among proteins whose sequence similarities often fall below the level of statistical signi cance but whose relationships are nonetheless biologically signi cant.