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Two-dimensional maps of contacts summarize interactions between amino acids in the structure. They reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of the residue contact maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity.
PROTMAP2D is a tool for calculation, visualization and comparison of contact maps. It can be used for quantitative and qualitative characterization of differences and similarities between alternative models of the same protein, e.g. members of the ensemble calculated from the results of the nuclear magnetic resonance (NMR) analysis, crystal structures solved under different conditions, theoretical models calculated with different programs, or series of conformations obtained in the course of molecular dynamics (MD) simulations. PROTMAP2D allows analyzing multimeric proteins, and can be used to visualize intermolecular contacts in protein-protein complexes.
The MacOSX and Windows standalone binary versions of PROTMAP2D are available for download. Linux binary bundle has some prerequisites to install (see the README file enclosed for details).
Program's ftp directory:
ftp://ftp.genesilico.pl/pub/software/protmap2d/
PROTMAP2D is available for academic users under the license (details enclosed in the license file to be found in each package). Non-academic users and those, who do not accept the license, may NOT download or use the software. A separate commercial license will be issued in the future.
We would greatly appreciate feedback from users, including compliments, bug reports, suggestions for new options to be implemented, etc. Send your messages to Michal J. Pietal, the principal developer of PROTMAP2D
PROTMAP2D gallery
A simple contact map of a dimer 1acv. Secondary structure visible (red bars- helices, green bars- sheets) was read out from the pdb file
A distance map of the first model of an NMR ensemble 1aca
Distance map of 1aca, cropped by lower and upper contact threshold, 7 and 20 A, respectively
A comparison two models of I-TevI catalytic domain. Right-upper: x-ray model (Van Roey, et al., 2002), left-lower: de-novo prediction (Bujnicki, et al., 2001)
A two-layer contact map on a 1acv ensemble. White contacts exist in all models, while grey exist only in some
Frequency contact map of a MD unfolding trajectory. Left-lower contacts co-exist in a native (starting) structure, whilst right-upper do not
A comparison of two MD unfolding trajectories (same parameters, temperature set to 300 and 500 K). Direction of the colour shift show stability of the structure during time (x and y axes)
A contact map similarity calculated for MD trajcetory
500.mpg
A MD trajectory movie exported to a file (feature available on windows and linux only)
NOTE: To open this file you not only need an appropriate MPEG file player, but also adequate video codecs installed. An example cross-platform tool capable of playing PROTMAP2D movie files is VLC program to be downloaded from http://www.videolan.org/vlc/
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