Documentation

The Bio3D package for structural bioinformatics consists of sets of functions for:

• input/output,
• sequence analysis,
• structure analysis,
• simulation analysis,
• normal mode analysis,
• correlation network analysis,
• format conversion and data manipulation, and
• graphics and visualization..

Major functions are listed below with links to further documentation that includes example code and results.

Note that you can also get help on any particular function by using the command ?function or help(function) (e.g. help(read.pdb)) and directly execute the example code for a given function with the command example(function) from within R itself.

We also distribute a number of extended Bio3D vignettes that provide worked examples of using Bio3D to perform a particular type of analysis. Currently available vignettes include:

• Installing Bio3D ( PDF | HTML)
• Getting started with Bio3D ( PDF | HTML )
• PDB structure manipulation and analysis with Bio3D ( PDF | HTML)
• Beginning trajectory analysis with Bio3D ( PDF | HTML)
• Enhanced methods for Normal Mode Analysis with Bio3D ( PDF | HTML)
• Comparative sequence and structure analysis with Bio3D ( PDF | HTML)
• Correlation network analysis with Bio3D ( PDF | HTML )
• Protein structure network analysis with Bio3D ( PDF | HTML )
• Online protein structure analysis with the Bio3D WebApp ( PDF | HTML )
• Online Normal Mode Analysis with Bio3D WebApps ( PDF | HTML )

There is also a package manual (in PDF format) that is a concatenation of each functions documentation.

Note that for information on Bio3D development status or to report a bug, please refer to: https://bitbucket.org/Grantlab/bio3d

Help topics

Input/Output:

Read and Write Common Biomolecular Data Types

• read.pdb(read.pdb2, print.pdb, summary.pdb): Read PDB File
• read.fasta: Read FASTA formated Sequences
• read.fasta.pdb: Read Aligned Structure Data
• read.ncdf: Read AMBER Binary netCDF files
• read.dcd: Read CHARMM/X-PLOR/NAMD Binary DCD files
• read.crd: Read Coordinate Data from Amber or Charmm
• read.pqr: Read PQR File
• read.mol2(print.mol2): Read MOL2 File
• read.all: Read Aligned Structure Data
• read.pdcBD: Read PQR output from pdcBD File
• read.cif: Read mmCIF File
• read.crd.amber: Read AMBER Coordinate files
• read.crd.charmm: Read CRD File
• read.prmtop(print.prmtop): Read AMBER Parameter/Topology files
• aln2html: Create a HTML Page For a Given Alignment
• get.pdb: Download PDB Coordinate Files
• get.seq: Download FASTA Sequence Files
• load.enmff(ff.calpha, ff.anm, ff.pfanm, ff.sdenm, ff.reach, ff.aaenm, ff.aaenm2): ENM Force Field Loader
• write.pdb: Write PDB Format Coordinate File
• write.crd: Write CRD File
• write.fasta: Write FASTA Formated Sequences
• write.ncdf: Write AMBER Binary netCDF files
• write.pqr: Write PQR Format Coordinate File
• write.pir: Write PIR Formated Sequences
• write.mol2: Write MOL2 Format Coordinate File
• pymol(pymol.pdbs, pymol.nma, pymol.pca, pymol.modes, pymol.dccm): Biomolecular Visualization with PyMOL
• vmd(vmd.cna, vmd.cnapath): View CNA Protein Structure Network Community Output in VMD

Sequence Analysis:

Do Interesting Things with Protein Sequence

• consensus: Sequence Consensus for an Alignment
• conserv: Score Residue Conservation At Each Position in an Alignment
• blast.pdb(get.blast, plot.blast): NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
• hmmer: HMMER Sequence Search
• pfam: Download Pfam FASTA Sequence Alignment
• uniprot: Fetch UniProt Entry Data.
• entropy: Shannon Entropy Score
• filter.identity: Percent Identity Filter
• seqidentity: Percent Identity
• motif.find: Find Sequence Motifs.
• pdbaln: Sequence Alignment of PDB Files
• seq2aln: Add a Sequence to an Existing Alignmnet
• seqaln: Sequence Alignment with MUSCLE
• seqaln.pair: Sequence Alignment of Identical Protein Sequences
• seqbind: Combine Sequences by Rows Without Recycling

Structure Analysis:

Do Interesting Things with Protein Structure

• angle.xyz: Calculate the Angle Between Three Atoms
• biounit:Biological Units Construction
• blast.pdb(get.blast, plot.blast): NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
• atom.select(atom.select.pdb, atom.select.mol2, atom.select.prmtop, print.select): Atom Selection from PDB and PRMTOP Structure Objects
• combine.select: Combine Atom Selections From PDB Structure
• cmap(cmap.default, cmap.xyz, cmap.pdb): Contact Map
• filter.cmap: Contact Map Consensus Filtering
• core.find(core.find.default, core.find.pdbs, core.find.pdb): Identification of Invariant Core Positions
• com(com.pdb, com.xyz): Center of Mass
• dccm: DCCM: Dynamical Cross-Correlation Matrix
• filter.dccm: Filter for Cross-correlation Matrices (Cij)
• dist.xyz: Calculate the Distances Between the Rows of Two Matrices
• dm(dm.pdb, dm.xyz, dm.pdbs): Distance Matrix Analysis
• dssp(dssp.pdb, dssp.pdbs, dssp.xyz, stride, print.sse): Secondary Structure Analysis with DSSP or STRIDE
• geostas(geostas.default, geostas.xyz, geostas.nma, geostas.enma, geostas.pdb, geostas.pdbs, amsm.xyz, print.geostas): GeoStaS Domain Finder
• mustang: Structure-based Sequence Alignment with MUSTANG
• fit.xyz(rot.lsq): Coordinate Superposition
• binding.site: Binding Site Residues
• mktrj(mktrj.pca, mktrj.nma, mktrj.enma): PCA / NMA Atomic Displacement Trajectory
• overlap: Overlap analysis
• pca: Principal Component Analysis
• pca.xyz(print.pca): Principal Component Analysis
• pca.pdbs: Principal Component Analysis
• pca.array: Principal Component Analysis of an array of matrices
• pca.tor: Principal Component Analysis
• dccm.pca: Dynamic Cross-Correlation from Principal Component Analysis
• project.pca(z2xyz.pca, xyz2z.pca): Project Data onto Principal Components
• pdbaln: Sequence Alignment of PDB Files
• pdb.annotate(pdb.pfam): Get Customizable Annotations From PDB Or PFAM Databases
• pdb2aln: Align a PDB structure to an existing alignment
• pdb2aln.ind: Mapping from alignment positions to PDB atomic indices
• pdb2sse:Obtain An SSE Sequence Vector From A PDB Object
• pdbs2sse: SSE annotation for a PDBs Object
• pdbfit(pdbfit.pdb, pdbfit.pdbs): PDB File Coordinate Superposition
• chain.pdb: Find Possible PDB Chain Breaks
• convert.pdb:Renumber and Convert Between Various PDB formats
• rgyr: Radius of Gyration
• rmsd: Root Mean Square Deviation
• filter.rmsd: RMSD Filter
• rmsf: Atomic RMS Fluctuations
• rmsip(rmsip.default, rmsip.enma): Root Mean Square Inner Product
• struct.aln: Structure Alignment Of Two PDB Files
• torsion.pdb: Calculate Mainchain and Sidechain Torsion/Dihedral Angles
• torsion.xyz: Calculate Torsion/Dihedral Angles
• wrap.tor: Wrap Torsion Angle Data
• aa2mass: Amino Acid Residues to Mass Converter
• aa.table: Table of Relevant Amino Acids
• atom.index: Atom Names/Types
• atom2mass(atom2mass.default, atom2mass.pdb): Atom Names/Types to Mass Converter
• atom2ele(atom2ele.default, atom2ele.pdb): Atom Names/Types to Atomic Symbols Converter
• cov.nma(cov.enma): Calculate Covariance Matrix from Normal Modes
• dccm.enma: Cross-Correlation for Ensemble NMA (eNMA)
• dccm.nma: Dynamic Cross-Correlation from Normal Modes Analysis
• dccm.xyz(cov2dccm): DCCM: Dynamical Cross-Correlation Matrix
• deformation.nma: Deformation Analysis
• fluct.nma: NMA Fluctuations
• inner.prod: Mass-weighted Inner Product
• load.enmff(ff.calpha, ff.anm, ff.pfanm, ff.sdenm, ff.reach, ff.aaenm, ff.aaenm2): ENM Force Field Loader
• nma: Normal Mode Analysis
• nma.pdb(build.hessian, print.nma): Normal Mode Analysis
• nma.pdbs(print.enma): Ensemble Normal Mode Analysis
• normalize.vector: Mass-Weighted Normalized Vector
• pdbs2pdb: PDBs to PDB Converter
• plot.enma: Plot eNMA Results
• plot.nma: Plot NMA Results
• plot.rmsip: Plot RMSIP Results
• sdENM: Index for the sdENM ff
• sse.bridges: SSE Backbone Hydrogen Bonding
• var.xyz(var.pdbs): Pairwise Distance Variance in Cartesian Coordinates
• inspect.connectivity: Check the Connectivity of Protein Structures

Trajectory Analysis:

Do Interesting Things with Simulation Data

• angle.xyz: Calculate the Angle Between Three Atoms
• cmap(cmap.default, cmap.xyz, cmap.pdb): Contact Map
• filter.cmap: Contact Map Consensus Filtering
• core.find(core.find.default, core.find.pdbs, core.find.pdb): Identification of Invariant Core Positions
• dccm: DCCM: Dynamical Cross-Correlation Matrix
• dccm.pca: Dynamic Cross-Correlation from Principal Component Analysis
• filter.dccm: Filter for Cross-correlation Matrices (Cij)
• lmi: LMI: Linear Mutual Information Matrix
• dist.xyz: Calculate the Distances Between the Rows of Two Matrices
• dm(dm.pdb, dm.xyz, dm.pdbs): Distance Matrix Analysis
• geostas(geostas.default, geostas.xyz, geostas.nma, geostas.enma, geostas.pdb, geostas.pdbs, amsm.xyz, print.geostas): GeoStaS Domain Finder
• fit.xyz(rot.lsq): Coordinate Superposition
• mktrj(mktrj.pca, mktrj.nma, mktrj.enma): PCA / NMA Atomic Displacement Trajectory
• overlap: Overlap analysis
• project.pca(z2xyz.pca, xyz2z.pca): Project Data onto Principal Components
• pca.tor: Principal Component Analysis
• pca.xyz(print.pca): Principal Component Analysis
• pdbaln: Sequence Alignment of PDB Files
• rgyr: Radius of Gyration
• rmsd: Root Mean Square Deviation
• filter.rmsd: RMSD Filter
• rmsf: Atomic RMS Fluctuations
• rmsip(rmsip.default, rmsip.enma): Root Mean Square Inner Product
• torsion.pdb: Calculate Mainchain and Sidechain Torsion/Dihedral Angles
• torsion.xyz: Calculate Torsion/Dihedral Angles
• wrap.tor: Wrap Torsion Angle Data

Normal Mode Analysis:

Probe Large-Scale Protein Motions

• aa2mass: Amino Acid Residues to Mass Converter
• aa.table: Table of Relevant Amino Acids
• atom.index: Atom Names/Types
• atom2mass(atom2mass.default, atom2mass.pdb): Atom Names/Types to Mass Converter
• atom2ele(atom2ele.default, atom2ele.pdb): Atom Names/Types to Atomic Symbols Converter
• bhattacharyya(bhattacharyya.nma, bhattacharyya.pca, bhattacharyya.enma, bhattacharyya.array, bhattacharyya.matrix): Bhattacharyya Coefficient
• cov.nma(cov.enma): Calculate Covariance Matrix from Normal Modes
• covsoverlap(covsoverlap.enma, covsoverlap.nma): Covariance Overlap
• dccm.enma: Cross-Correlation for Ensemble NMA (eNMA)
• dccm.nma: Dynamic Cross-Correlation from Normal Modes Analysis
• dccm.xyz(cov2dccm): DCCM: Dynamical Cross-Correlation Matrix
• deformation.nma: Deformation Analysis
• geostas(geostas.default, geostas.xyz, geostas.nma, geostas.enma, geostas.pdb, geostas.pdbs, amsm.xyz, print.geostas): GeoStaS Domain Finder
• fluct.nma: NMA Fluctuations
• inner.prod: Mass-weighted Inner Product
• load.enmff(ff.calpha, ff.anm, ff.pfanm, ff.sdenm, ff.reach, ff.aaenm, ff.aaenm2): ENM Force Field Loader
• mktrj(mktrj.pca, mktrj.nma, mktrj.enma): PCA / NMA Atomic Displacement Trajectory
• nma: Normal Mode Analysis
• nma.pdb(build.hessian, print.nma): Normal Mode Analysis
• nma.pdbs(print.enma): Ensemble Normal Mode Analysis
• aanma(aanma.pdb, rtb):All Atom Normal Mode Analysis
• aanma.pdbs:Ensemble Normal Mode Analysis with All-Atom ENM
• gnm(gnm.pdb, gnm.pdbs):Gaussian Network Model
• dccm.gnm(dccm.egnm):Dynamic Cross-Correlation from Gaussian Network Model
• normalize.vector: Mass-Weighted Normalized Vector
• pdbs2pdb: PDBs to PDB Converter
• plot.enma: Plot eNMA Results
• plot.nma: Plot NMA Results
• plot.rmsip: Plot RMSIP Results
• sdENM: Index for the sdENM ff
• sse.bridges: SSE Backbone Hydrogen Bonding
• sip(sip.default, sip.nma, sip.enma): Square Inner Product
• var.xyz(var.pdbs): Pairwise Distance Variance in Cartesian Coordinates

Correlation Network Analysis:

Network analysis of dynamic coupling

• cna(cna.dccm, cna.ensmb): Protein Dynamic Correlation Network Construction and Community Analysis.
• cnapath(summary.cnapath, print.cnapath): Suboptimal Path Analysis for Correlation Networks
• dccm: DCCM: Dynamical Cross-Correlation Matrix
• lmi: LMI: Linear Mutual Information Matrix
• filter.dccm: Filter for Cross-correlation Matrices (Cij)
• cmap(cmap.default, cmap.xyz, cmap.pdb): Contact Map
• community.tree: Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object.
• network.amendment: Amendment of a CNA Network According To A Input Community Membership Vector.
• plot.cna: Protein Structure Network Plots in 2D and 3D.
• print.cna(summary.cna): Summarize and Print Features of a cna Network Graph
• identify.cna: Identify Points in a CNA Protein Structure Network Plot
• layout.cna: Protein Structure Network Layout
• prune.cna: Prune A cna Network Object
• community.aln:Align communities from two or more networks

Graphics:

Plotting and Graphic Display

• bwr.colors(mono.colors): Color Palettes
• vmd_colors: VMD Color Palette
• plot.bio3d(plotb3): Plots with marginal SSE annotation
• plot.cmap: Plot Contact Matrix
• plot.core: Plot Core Fitting Progress
• plot.dccm: DCCM Plot
• plot.dmat: Plot Distance Matrix
• plot.fluct: Plot Fluctuations
• plot.geostas: Plot Geostas Results
• plot.pca(plot.pca.score, plot.pca.scree): Plot PCA Results
• plot.pca.loadings: Plot Residue Loadings along PC1 to PC3
• hclustplot: Dendrogram with Clustering Annotation
• plot.cna: Protein Structure Network Plots in 2D and 3D.
• plot.fasta: Plot a Multiple Sequence Alignment
• plot.hmmer: Plot a Summary of HMMER Hit Statistics.
• plot.matrix.loadings:Plot Residue-Residue Matrix Loadings

Utilities:

Convert and Manipulate Data

• aa.index: AAindex: Amino Acid Index Database
• aa123(aa321): Convert Between 1-letter and 3-letter Aminoacid Codes
• aa2index: Convert an Aminoacid Sequence to AAIndex Values
• aln2html: Create a HTML Page For a Given Alignment
• as.fasta: Alignment to FASTA object
• as.pdb(as.pdb.mol2, as.pdb.prmtop, as.pdb.default): Convert to PDB format
• as.select: Convert Atomic Indices to a Select Object
• atom.select(atom.select.pdb, atom.select.mol2, atom.select.prmtop, print.select): Atom Selection from PDB and PRMTOP Structure Objects
• combine.select: Combine Atom Selections From PDB Structure
• atom2xyz(xyz2atom): Convert Between Atom and xyz Indices
• basename.pdb:
• bio3d-package(bio3d): Biological Structure Analysis
• biounit:Biological Units Construction
• bounds: Bounds of a Numeric Vector
• bounds.sse:Obtain A SSE Object From An SSE Sequence Vector
• cat.pdb: Concatenate Multiple PDB Objects
• check.utility: Check on Missing Utility Programs
• clean.pdb:Inspect And Clean Up A PDB Object
• chain.pdb: Find Possible PDB Chain Breaks
• convert.pdb:Renumber and Convert Between Various PDB formats
• diag.ind: Diagonal Indices of a Matrix
• difference.vector: Difference Vector
• gap.inspect: Alignment Gap Summary
• inspect.connectivity: Check the Connectivity of Protein Structures
• filter.identity: Percent Identity Filter
• is.gap: Gap Characters
• is.pdb(is.pdbs): Is an Object of Class
• is.select:Is an Object of Class
• is.xyz(as.xyz): Is an Object of Class
• is.mol2: Is an Object of Class
• lbio3d: List all Functions in the bio3d Package
• mask(mask.dccm): Mask a Subset of Atoms in a DCCM Object.
• orient.pdb: Orient a PDB Structure
• pairwise: Pair Indices
• plot.bio3d(plotb3): Plots with marginal SSE annotation
• print.core: Printing Core Positions and Returning Indices
• print.cna(summary.cna): Summarize and Print Features of a cna Network Graph
• print.fasta(.print.fasta.ali): Printing Sequence Alignments
• print.xyz: Printing XYZ coordinates
• rle2(print.rle2):Run Length Encoding with Indices
• filter.rmsd: RMSD Filter
• pdbseq: Extract The Aminoacid Sequence From A PDB Object
• seqbind: Combine Sequences by Rows Without Recycling
• pdbsplit: Split a PDB File Into Separate Files, One For Each Chain.
• store.atom: Store all-atom data from a PDB object
• trim(trim.pdb): Trim a PDB Object To A Subset of Atoms.
• trim.mol2: Trim a MOL2 Object To A Subset of Atoms.
• trim.pdbs: Filter or Trim a PDBs Object
• trim.xyz: Trim a XYZ Object of Cartesian Coordinates.
• unbound: Sequence Generation from a Bounds Vector
• vec2resno: Replicate Per-residue Vector Values
• setup.ncore: Setup for Running Bio3D Functions using Multiple CPU Cores
• elements:Periodic Table of the Elements
• formula2mass:Chemical Formula to Mass Converter

Example Data:

Bio3d Example Data

• example.data(kinesin, transducin, pdbs, core, annotation, hivp):Bio3d Example Data