Analysis of Energy Landscapes with Barriers and Friends


barrier tree

The barriers program

The program  barriers  reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by  RNAsubopt  For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation and basin sizes can be included via options. A PostScript drawing of the resulting tree is written to "tree.ps" in the current directory.

For detailed instructions see the man page.

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source code of program barriers release 1.5.2

treekin example

The treekin program

The program  treekin  computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix). For detailed instructions see the man page.

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source code of program  treekin  release 0.3.1

The bar_map program

The program  bar_map  computes a mapping between a series of barrier trees as computed by the barriers program. This of interest in particular in the context of co-transcriptional folding, where the one can compute barrier trees corresponding to different length partial transcripts; or for dynamic landscapes produced e.g. when varying the temperature.

The mapping produced by bar_map can be used in conjunction with treekin to compute folding dynamics on time-varying landscape. In the case of co-transcriptional folding, for example, treekin is used to compute folding dynamics for the length of 1 elongation step, the bar_map mapping is then used to transfer the final population onto the next (longer) landscape and thus to obtain the initial condition for the next treekin computation.

For detailed instructions see the man page.

To simplify using bar_map in conjunction with treekin, the barmap_simulator utility produces shell script containing treekin commands for a complete simulation run.

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bar_map and barmap_simulator Perl code.