| Type: | Package |
| Title: | Conformational Manipulations of Protein Atomic Structures |
| Version: | 0.1.1 |
| Date: | 2022-01-08 |
| Author: | Samuel W.K. Wong, Dylan Shi, Megan Hazlett, Jasmine Cheng |
| Maintainer: | Samuel W.K. Wong <samuel.wong@uwaterloo.ca> |
| Description: | Manipulate and analyze 3-D structural geometry of Protein Data Bank (PDB) files. |
| License: | GPL-3 |
| Imports: | Rcpp (≥ 0.12.18), bio3d |
| LinkingTo: | Rcpp, RcppEigen |
| RoxygenNote: | 6.1.1 |
| LazyData: | true |
| Depends: | R (≥ 3.2.0) |
| NeedsCompilation: | yes |
| Packaged: | 2022-01-08 22:35:00 UTC; s246wong |
| Repository: | CRAN |
| Date/Publication: | 2022-01-09 00:02:41 UTC |
Atom parameters and definitions for side chains
Description
List of the atom dependencies and typical bond parameters in protein structures for side chains of the 20 standard amino acid types.
Usage
atomdeps
Format
A list for the 20 amino acid types, each having the attributes
"tangle": Dihedral angle defined by atoms A-B-C-D as described below.
NA's represent the free side chain dihedral angles chi for that amino acid."names": The component atoms of the amino acid side chain. Represents atom D in the dihedral.
"matx": The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".
"bangle": Planar bond angle formed between B-C-D
"blength": Bond length between C-D
References
Engh, Richard A., and Robert Huber. "Accurate bond and angle parameters for X-ray protein structure refinement." Acta Crystallographica Section A 47.4 (1991): 392-400.
Atom Type Table
Description
Table listing the 167 standard atom types in protein structures (amino acid type and atom identifier pairs). Hydrogen atoms are not considered.
Usage
atomtype
Format
A two-column data frame, with "resid" providing the 3-letter amino acid abbreviation and "atomid" providing the component atoms of each amino acid.
Source
PDB ATOM entry: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
Calculate Cartesian coordinates for 1-4 bonded atoms
Description
Consider atoms A-B-C-D forming a dihedral. Given coordinates for atoms A,B,C of the dihedral, the dihedral angle, bond angle, and bond length, calculate the Cartesian coordinates of atom D in the dihedral.
Usage
calCo(prev_atoms, length, bAngle, tAngle)
Arguments
prev_atoms |
a 3x3 matrix of coordinates for atoms A-B-C in dihedral, listed by row |
length |
bond length between atoms C-D in dihedral |
bAngle |
planar bond angle between atoms B-C-D (in degrees) |
tAngle |
dihedral angle formed by atoms A-B-C-D (in degrees) |
Value
Returns the vector of coordinates for the fourth atom in the dihedral
Examples
prevAtoms <- matrix(c(50.051, 37.144, -4.723,
50.044, 36.248, -3.559,
51.296, 35.369, -3.476), nrow=3, ncol=3, byrow=TRUE)
calCo(prevAtoms, length=1.33, bAngle=116.8, tAngle=-25.3)
Calculate Cartesian coordinates of side chains
Description
Rotates the free side chain dihedral angles of an amino acid to the specified values. Calculates the updated Cartesian coordinates of all the atoms of that amino acid side chain.
Usage
calscco(pdb, resno, chi)
Arguments
pdb |
A PDB object |
resno |
The residue number of the amino acid side chain to rotate |
chi |
A vector of dihedral angles (in degrees), with length matching the number of free side chain dihedral angles for that amino acid type. See atomdeps for definitions. |
Details
Calls calCo successively for each atom in the amino acid side chain, using the bond parameters defined in atomdeps.
Value
Returns a PDB object with updated coordinates of side chain atoms in "resno".
Examples
## Position 10 of nat879 is ASP with 2 side chain dihedrals chi1 and chi2
nat879$atom[nat879$atom$resno==10,]
pdbn <- calscco(nat879,10,c(60.0,-80.0))
pdbn$atom[pdbn$atom$resno==10,]
DFIRE Energy Evaluation for Protein Conformations
Description
Calculates the energy of a protein conformation using the DFIRE potential.
Usage
dfireE(pdb)
Arguments
pdb |
A PDB object, read using read.pdb. |
Value
Returns the DFIRE energy.
References
Zhou, Hongyi, and Yaoqi Zhou. "Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction." Protein science 11.11 (2002): 2714-2726.
Examples
dfireE(nat879)
Sample Protein Conformation 1
Description
A sample protein conformation in PDB format. Excerpted from the native structure of CASP12 target 879, residues 5-24
Usage
nat879
Format
A PDB object, read using read.pdb
Source
CASP12 data archive on Prediction Center: http://predictioncenter.org/download_area/CASP12/targets/casp12.targets_T0.releaseDec022016.tgz
Root Mean Squared Deviation (RMSD) of Two Protein Conformations
Description
RMSD calculation between the atoms of two PDB objects.
Usage
pdbrmsd(pdb1, pdb2, start, end, type='all', optimal=FALSE)
Arguments
pdb1 |
PDB object containing reference coordinates of atoms in protein conformation. |
pdb2 |
PDB object containing coordinates of atoms in protein conformation to compare with pdb1. |
start |
The starting residue position for the RMSD calculation. If not supplied, defaults to first residue of chain. |
end |
The ending residue position for the RMSD calculation. If not supplied, defaults to final residue of chain. |
type |
Specifies atoms to be included in the calculation. Can be 'all', 'CA' (CA atoms only), or 'backbone' (CA, N, C, O). |
optimal |
Apply optimal rotation and superposition? As described in https://cnx.org/contents/HV-RsdwL@23/Molecular-Distance-Measures |
Details
Similar to rmsd, but with implementation in C++.
Value
Returns a list with calculated RMSD value and the optimal rotation matrix.
Examples
pdbrmsd(nat879, pred879, start=10, end=20, 'all', optimal=TRUE)
Sample Protein Conformation 2
Description
A sample protein conformation in PDB format. Excerpted from a structure prediction of CASP12 target 879, residues 5-24
Usage
pred879
Format
A PDB object, read using read.pdb
Source
CASP12 data archive on Prediction Center: http://predictioncenter.org/download_area/CASP12/targets/casp12.targets_TR.releaseDec022016.tgz
Calculate dihedral angle formed by four atoms
Description
For Cartesian coordinates of atoms A-B-C-D, calculate the dihedral angle formed by viewing down the B-C axis.
Usage
torsion(a, b, c, d)
Arguments
a |
length 3 vector of coordinates of atom A |
b |
length 3 vector of coordinates of atom B |
c |
length 3 vector of coordinates of atom C |
d |
length 3 vector of coordinates of atom D |
Details
Similar to torsion.xyz, but with implementation in C++.
Value
Returns the dihedral angle (in degrees between -180 and 180).
Examples
torsion(c(50.051, 37.144, -4.723), c(50.044, 36.248, -3.559),
c(51.296, 35.369, -3.476), c(51.930,35.119,-4.618))