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Documentation for the MakeRotLib application
Author
P. Douglas Renfrew (renfr.nosp@m.ew@n.nosp@m.yu.ed.nosp@m.u)

Metadata

The documentation was last updated in December 2011, by P. Douglas Renfrew. The PI for this application is Brian Kuhlman (bkuhl.nosp@m.man@.nosp@m.email.nosp@m..unc.nosp@m..edu).

Code and Demo

The main mover is located in the application code at rosetta_source/src/protocols/make_rot_lib. The application code is located at rosetta_source/src/apps/public/ncaa_utilities/make_rot_lib.cc. The integration tests can be found at rosetta_tests/integration/tests/make_rot_lib/. The demo can be found at rosetta_demos/make_rot_lib/.

References

P. Douglas Renfrew, Eun Jung Choi, Brian Kuhlman, "Using Noncanonical Amino Acids in Computational Protein-Peptide Interface Design" (2011) PLoS One. It is strongly recomended to read the paper as it provided addition details.

New_Library contains code for this purpose

This code creats a Noncanonical Amino Acid (NCAA) rotamer library and is the second of three steps toward being able to use a NCAA in Rosetta.

Algorithm

Rotamer libraries are sets of common side chain conformations that generally correspond to local minima on the side chain conformational energy landscape. Side chain conformations are usually represented as a set of mean angles and a standard deviation to indicate variability. Rotamer libraries are used in for two main purposes in Rosetta: to provide starting points for side chain optimization routines, and the relative frequency is used as a pseudo-energy. Traditionally rotamer libraries are created by collecting statistics from protein structures. Rosetta uses the backbone dependent Drunbrack rotamer libraries. Since there are not enough structures containing NCAAs they must be generated.

Running the MakeRotLib protocol consists of four steps

Limitations

This code is designed to make Dunbrack 2002 style rotamer libraies for noncanonical side chains with an alpha-peptide backbone.

Input Files

Rosetta primarily uses backbone dependent rotamer libraries. Backbone-dependent rotamer libraries list provide side chain conformations sampled from residue positions whose backbone dihedral angles fall in particular bins. In the case of the Drunbrack rotamer libraries used by Rosetta the bins are in 10 degree intervals for for both phi and psi for a total of 1296 (36*36) phi/psi bins. To replicate this for the NCAAs we need to create a set of side chain rotamers for each member of a set of phi/psi bins.

The MakeRotLib protocol takes an option file as input. It requires an options file for each phi/psi bin. The first step in running it is creating these 1296 options files. Continuing from the HowToMakeResidueTypeParamFiles protocol capture we are again using ornithine as an example. Ornithine has 3 sidechain dihedral angles (chi). We want to sample each chi angle from 0 to 360 degrees in 30 degree intervals, and based on the chemistry of the side chain we predict that were will probably be three preferred angles for each chi angle at 60, 180, and 300 degrees for a total of 27 rotamers (3x3x3). We setup our MakeRotLib options file template as shown bellow.

The C40_rot_lib_options_XXX_YYY.in file is shown bellow.

AA_NAME C40
PHI_RANGE XXX XXX 0
PSI_RANGE YYY YYY 0
NUM_CHI 3
CHI_RANGE 1 0  330  30
CHI_RANGE 2 0  330  30
CHI_RANGE 3 0  330  30
CENTROID 300 1 300 1 300 1
CENTROID 300 1 300 1 180 2
CENTROID 300 1 300 1  60 3
CENTROID 300 1 180 2 300 1
CENTROID 300 1 180 2 180 2
CENTROID 300 1 180 2  60 3
CENTROID 300 1  60 3 300 1
CENTROID 300 1  60 3 180 2
CENTROID 300 1  60 3  60 3
CENTROID 180 2 300 1 300 1
CENTROID 180 2 300 1 180 2
CENTROID 180 2 300 1  60 3
CENTROID 180 2 180 2 300 1
CENTROID 180 2 180 2 180 2
CENTROID 180 2 180 2  60 3
CENTROID 180 2  60 3 300 1
CENTROID 180 2  60 3 180 2
CENTROID 180 2  60 3  60 3
CENTROID  60 3 300 1 300 1
CENTROID  60 3 300 1 180 2
CENTROID  60 3 300 1  60 3
CENTROID  60 3 180 2 300 1
CENTROID  60 3 180 2 180 2
CENTROID  60 3 180 2  60 3
CENTROID  60 3  60 3 300 1
CENTROID  60 3  60 3 180 2
CENTROID  60 3  60 3  60 3

To generate the 1296 input files we use a provided script that simply replace the XXX and YYY with the phi and psi values. The script is run as shown bellow.

$ cd inputs
$ ../scripts/make_inputs C40_rot_lib_options_XXX_YYY.in

The number of chi angles and the CHI_RANGE sampling interval are the primary determinants of the run time as they determine the number of rotamers that will be tested for each phi/psi bin. It is recommended to have at least 500 samples per chi. In the ornithine example we sample in 30 degree intervals for each of the 3 chi angles giving us a total of 1728 (12x12x12) conformations tested for each phi/psi bin. For a residue with a single chi 1 degree bins will suffice.

Running the MakeRotLib Protocol

The next step is to run the MakeRotLib protocol on each of the input files we created in step one. This is the most time consuming portion of the process and should probably be done on a cluster. As cluster setups vary, an example for a single MakeRotLib options file is provided. The other 1295 should be run identically.

$ cd outputs
$ PATH/TO/ROSETTA/bin/make_rot_lib.macosgccrelease -database PATH/TO/rosetta_database -rot_lib_options_file ../inputs/C40_rot_lib_options_-60_-40.in >& C40_rot_lib_options_-60_-40.log &

Note: The extension on your executable maybe different.

The only options passed to the executable are the path to the database and the MakeRotLib options file. After the run completes a file called C40_-60_-40_bbdep.rotlib should be in the output directory. This is the backbone dependent rotamer library for a phi of -60 and a psi of -40.

The log file from the rosetta run in includes quite a bit of useful output.

There are three main sections to the log output, ROTAMERS, CENTROIDS and FINAL ROTAMERS sections. Each one shows the following data: phi, psi, omega and epsilon backbone dihedral angles, probability, total energy, torsion energy, intra-residue repulsive, intra-residue attractive, the number of chi angles, the assigned cluster number, the set of input chi angles, the set of minimized chi angles, the standard deviation, and the distance from that point to each of the cluster centroids.

The log file also displays the number of conformations per cluster, the average distance between the cluster center and the members of that cluster. Lack of conformations in a cluster and a large (>30) average cluster centroid distance suggests that that cluster is higher in energy.

Options

The MakeRotlib protocol has one option and it is not really optional.

Expected Outputs

You should have 1296 rotamer libraries, one for each phi/psi bin.

Assembilng the Individual Rotamer Libraries in to a Single File

After the MakeRotLib protocol has been run on all of the MakeRotLib options files the individual rotamer libraries for each phi psi bin need to be assembled in to a single file. This is accomplished with a provided script as shown bellow.

$ cd outputs
$ ../scripts/make_final_from_phi_psi.pl C40

The single file rotamer library should be called C40.rotlib. The file should be placed in the ncaa_rotlibs directory in the database.

$ cp C40.rotlibs PATH/TO/DATABASE/rosetta_database/ncaa_rotlibs/

Modifying the ResidueType Paramater File

The last step is modifying the residue type parameter file to use the new rotamer library. To do this we need to add the name of the rotamer library, the number chi angles it describes, and how many bins there are for each chi angle to the Residue type parameter file. The ornithine rotamer library is called C40.rotlib and the rotamer library describes 3 chi angles and each of those 3 chi angle has 3 rotamer numbers. So we would use the following commands to add that information to the file we created in HowToMakeResidueTypeParamFiles.

$ echo "NCAA_ROTLIB_PATH C40.rotlib" >> PATH/TO/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/l-ncaa/ornithine.params
$ echo "NCAA_ROTLIB_NUM_ROTAMER_BINS 3 3 3 3" >> PATH/TO/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/l-ncaa/ornithine.params

New things since last release

This application is new for the Rosetta 3.4 release.