Rotamers

The Rotamers is a submodule of ProtoSyn.Peptides module. As such, the following section introduces both new types and methods that work together, in a generally independent way from the rest of the module, and require an unique exploratory section on their own.

A Rotamer is a collection of chi angles for a specific conformation for the sidechain of an aminoacid. Although virtually all dihedral angles are allowed, for each chi dihedral, certain conformations are energetically more favourable and therefore have a higher natural probability of observation. The allowed Rotamers can be further dependent on certain backbone dihedral angles (for the phi and psi dihedrals). All this information can be gathered in a Rotamer Library, a useful tool when trying to answer the question: "What set of sidechain conformations stabilize the protein structure?", sometimes also referred to as the sidechain packaging problem. Multiple such rotamer libraries have been proposed. ProtoSyn makes available a set of types and methods that allow the manipulation and application of rotamer libraries, while using, as a default, the 2011 Dunbrack library. This is further explored in the following section, sub-divided as follows for organizational purposes:

Organizing a Rotamer Library
Applying a Rotamer Library
Loading a Rotamer Library

Organizing a Rotamer Library

ProtoSyn.Peptides.Rotamer — Type

Rotamer{T <: AbstractFloat}(name::String, chis::Dict{AbstractSelection, Tuple{T, T}})

A Rotamer holds information regarding a single conformation for all chi dihedral angles of a sidechain belonging to an aminoacid identified by the given name. The chis list is, therefore, a dictionary, where the key is the AbstractSelection (chi1, chi2, chi3 or chi4) and the value is a Tuple{T, T}, where the first entry is the average dihedral angle and the second entry is the standard deviation expected for that dihedral angle.

See also

get_rotamer apply!

Examples

julia> rot_lib["LYS"][35°, -35°][1]
Rotamer{Float64}: LYS | Chi1:   -67.5° ±  6.9 | Chi2:  -179.6° ±  9.7 | Chi3:  -179.7° ± 11.8 | Chi4:   178.5° ± 12.0

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ProtoSyn.Peptides.BBI_RotamerLibrary — Type

BBI_RotamerLibrary{T <: AbstractFloat}(rotamers::Vector{Rotamer{T}}, weights::Weights{T, T, Array{T, 1}})

A BBI_RotamerLibrary is a backbone-independent list of Rotamer instances, ordered based on the natural probability of occurrence, where each position in the rotamers list has a corresponding position in the weights list.

See also

sample_rotamer

Examples

julia> rot_lib["VAL"][35°, -35°]

+---------------------------------------------------------------------------------------------------------------------------+
| Index | Probability | Rotamer description                                                                                 |
+---------------------------------------------------------------------------------------------------------------------------+
| 1     |      82.07% | VAL | Chi1:   175.8° ±  5.6 | Chi2: --              | Chi3: --              | Chi4: --              |
| 2     |      13.74% | VAL | Chi1:    64.7° ±  7.5 | Chi2: --              | Chi3: --              | Chi4: --              |
| 3     |       4.18% | VAL | Chi1:   -61.6° ±  6.4 | Chi2: --              | Chi3: --              | Chi4: --              |
+---------------------------------------------------------------------------------------------------------------------------+

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ProtoSyn.Peptides.BBD_RotamerLibrary — Type

BBD_RotamerLibrary{T <: AbstractFloat}(name::String, phis::Vector{T}, psis::Vector{T}, rotamer_stacks::Matrix{BBI_RotamerLibrary}) where {T <: AbstractFloat}

A BBD_RotamerLibrary is a 2D backbone dependent matrix of BBI_RotamerLibrary instances (rotamer_stacks), indexed by both the list of backbone phi dihedrals (phis) and the list of backbone psi dihedrals (psis). Each BBD_RotamerLibrary only hold information regarding one type of aminoacid, identified by the name. Each entry in the rotamer_stacks matrix only holds information of the list of rotamers available/plausible for a specific set of phi and psi backbone dihedrals.

See also

load_dunbrack

Examples

julia> rot_lib["VAL"]
Name: VAL | Shape: (37, 37)

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ProtoSyn Rotamer Library

Figure 1 | A diagram representation of a ProtoSyn Rotamer Library organization. For each entry in a dictionary (where the keys are the aminoacid names with a rotatable sidechain), a BBD_RotamerLibrary can be queried for with the backbone phi and psi dihedral angles, retrieving the backbone dependent BBI_RotamerLibrary. This object organizes all the plausible Rotamer conformations, based on the probability of natural occurrence, from where a specific Rotamer can be sampled. Finally, a Rotamer is simply a list of chi dihedral angles (and the corresponding standard deviation), and can be applied to a Pose (using the apply! method).

Applying a Rotamer Library

ProtoSyn.Peptides.apply! — Function

apply!(state::State, rotamer::Rotamer, residue::Residue)

Apply the given Rotamer rotamer to the sidechain of Residue residue, on the provided State state. Return the applied Rotamer rotamer, without applying the sync! method to the State state.

Examples

julia> ProtoSyn.Peptides.apply!(pose.state, rot_lib["GLU"][35°, -35°][1], pose.graph[1][2])
Rotamer{Float64}: GLU | Chi1:   -55.6° ±  0.0 | Chi2:   187.7° ±  0.0 | Chi3:    -2.6° ±  0.0 | Chi4: --

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ProtoSyn.Peptides.sample_rotamer — Function

sample_rotamer(rs::BBI_RotamerLibrary{T}, [n::Int = -1]) where {T <: AbstractFloat}

Sample a Rotamer instance from the given BBI_RotamerLibrary rs, taking the natural probability of occurrence into consideraction. If a n value is given, sample only from the n most likely Rotamer instances. If n is 0 or lower (-1, by default), sample from all Rotamer instances. Return the sampled Rotamer instance.

Examples

julia> ProtoSyn.Peptides.sample_rotamer(rot_lib["GLU"][35°, -35°])
Rotamer{Float64}: GLU | Chi1:   -66.8° ±  8.2 | Chi2:   179.1° ± 11.8 | Chi3:   -35.0° ±  8.5 | Chi4: --

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sample_rotamer(rl::Dict{String, BBI_RotamerLibrary}, residue::Residue, n::Int = -1)

Sample a Rotamer instance from the corresponding BBI_RotamerLibrary for the given Residue residue name. This method takes the natural probability of occurrence into consideraction. If a n value is given, sample only from the n most likely Rotamer instances. If n is 0 or lower (-1, by default), sample from all Rotamer instances. Return the sampled Rotamer instance.

Examples

julia> ProtoSyn.Peptides.sample_rotamer(rot_lib, pose.graph[1][24])
Rotamer{Float64}: SER | Chi1:   179.7° ±  8.4 | Chi2: --              | Chi3: --              | Chi4: --

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sample_rotamer(pose::Pose, rl::Dict{String, BBD_RotamerLibrary}, residue::Residue, [n::Int = -1], [random_inexistent_phi_psi::Bool = false])

Sample a Rotamer instance from the corresponding BBD_RotamerLibrary for the given Residue residue name. Since the BBD_RotamerLibrary is backbone-dependent, the current State of the provided Pose pose is read to sample a Rotamer. This method takes the natural probability of occurrence into consideraction. If a n value is given, sample only from the n most likely Rotamer instances. If n is 0 or lower (-1, by default), sample from all Rotamer instances. If random_inexistent_phi_psi is set to true (false, by default), randomly assigns a phi or psi angle value when none exists (for example, in terminal Residue instances), allowing for a Rotamer to still be sampled. Return the sampled Rotamer instance.

Examples

julia> ProtoSyn.Peptides.sample_rotamer(pose, rot_lib, pose.graph[1][6])
Rotamer{Float64}: GLU | Chi1:   -65.5° ±  9.5 | Chi2:    81.7° ±  9.6 | Chi3:     7.3° ±  8.5 | Chi4: --

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ProtoSyn.Peptides.get_rotamer — Function

get_rotamer(pose::Pose, residue::Residue)

Measure the existent chi dihedral angles in Residue residue on the given Pose pose, saving the information in a new Rotamer instance.

Examples

julia> ProtoSyn.Peptides.get_rotamer(pose, pose.graph[1][2])
Rotamer{Float64}: GLU | Chi1:   180.0° ±  0.0 | Chi2:  -180.0° ±  0.0 | Chi3:    90.0° ±  0.0 | Chi4: --

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Loading a Rotamer Library

ProtoSyn.Peptides.load_dunbrack — Function

load_dunbrack([::Type{T}], [filename::String]) where {T <: AbstractFloat}

Load a Dunbrack styled rotamer library from file filename (if no filename is given, will load the default rotamer library from the resources directory). If no type T is provided, will use ProtoSyn.Units.defaultFloat. Return a dictionary where each key is the name of an aminoacid type and the value is the corresponding loaded BBD_RotamerLibrary instance. Note that not all aminoacid types have sidechains, and therefore, have an associated BBD_RotamerLibrary instance.

Examples

julia> rot_lib = ProtoSyn.Peptides.load_dunbrack(Float64)
Dict{String, ProtoSyn.Peptides.BBD_RotamerLibrary} with 19 entries:
  "GLN" => Name: GLN | Shape: (37, 37)…
  "LYS" => Name: LYS | Shape: (37, 37)…
  "ASN" => Name: ASN | Shape: (37, 37)…
  "TRP" => Name: TRP | Shape: (37, 37)…
  "THR" => Name: THR | Shape: (37, 37)…
  "VAL" => Name: VAL | Shape: (37, 37)…
  "HIS" => Name: HIS | Shape: (37, 37)…
  "SER" => Name: SER | Shape: (37, 37)…
  "PRO" => Name: PRO | Shape: (37, 37)…
  "ASP" => Name: ASP | Shape: (37, 37)…
  "PHE" => Name: PHE | Shape: (37, 37)…
  "ILE" => Name: ILE | Shape: (37, 37)…
  "TYR" => Name: TYR | Shape: (37, 37)…
  "HIE" => Name: HIS | Shape: (37, 37)…
  "ARG" => Name: ARG | Shape: (37, 37)…
  "LEU" => Name: LEU | Shape: (37, 37)…
  "MET" => Name: MET | Shape: (37, 37)…
  ⋮     => ⋮

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