Recent applications such as CMView ( Vehlow et al., 2011) examine the nature of structural differences or changes in proteins through the use of residue–residue (RR) contact maps ( Holm and Sander, 1993). The rapid improvement of technology in recent decades has enhanced our knowledge of protein structure, as visualization software has revolutionized our understanding of molecular mechanisms. The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps.Īvailability and implementation: RRDistMaps was developed as part of UCSF Chimera release 1.10, which is freely available at, and operates on Linux, Windows, and Mac OS. Users can target residue pairs in RRDistMaps for further navigation in Chimera. hinge motion), between unbound and bound proteins through distance patterns. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. Binary (yes/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges. Motivation: Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification.
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