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

mktrj()

PCA / NMA Atomic Displacement Trajectory

pymol()

Biomolecular Visualization with PyMOL

vmd()

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() print(<select>)

Atom Selection from PDB and PRMTOP Structure Objects

combine.select()

Combine Atom Selections From PDB Structure

cmap()

Contact Map

filter.cmap()

Contact Map Consensus Filtering

core.find()

Identification of Invariant Core Positions

core.cmap()

Identification of Contact Map Core Positions

com()

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()

Distance Matrix Analysis

dssp() stride() print(<sse>)

Secondary Structure Analysis with DSSP or STRIDE

geostas() 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()

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>)

Dynamical Cross-Correlation Matrix 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()

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()

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()

Atom Names/Types to Mass Converter

atom2ele()

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>)

Dynamical Cross-Correlation Matrix from Cartesian Coordinates

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()

Contact Map

filter.cmap()

Contact Map Consensus Filtering

core.find()

Identification of Invariant Core Positions

dccm()

DCCM: Dynamical Cross-Correlation Matrix

dccm(<pca>)

Dynamical Cross-Correlation Matrix from Principal Component Analysis

filter.dccm()

Filter for Cross-correlation Matrices (Cij)

dist.xyz()

Calculate the Distances Between the Rows of Two Matrices

dm()

Distance Matrix Analysis

dssp() stride() print(<sse>)

Secondary Structure Analysis with DSSP or STRIDE

geostas() amsm.xyz() print(<geostas>)

GeoStaS Domain Finder

fit.xyz() rot.lsq()

Coordinate Superposition

mktrj()

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()

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()

Atom Names/Types to Mass Converter

atom2ele()

Atom Names/Types to Atomic Symbols Converter

bhattacharyya()

Bhattacharyya Coefficient

cov(<nma>) cov(<enma>)

Calculate Covariance Matrix from Normal Modes

covsoverlap()

Covariance Overlap

dccm(<enma>)

Cross-Correlation for Ensemble NMA (eNMA)

dccm(<nma>)

Dynamic Cross-Correlation from Normal Modes Analysis

dccm(<xyz>)

Dynamical Cross-Correlation Matrix from Cartesian Coordinates

deformation.nma()

Deformation Analysis

geostas() 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()

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() rtb()

All Atom Normal Mode Analysis

aanma(<pdbs>)

Ensemble Normal Mode Analysis with All-Atom ENM

gnm()

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()

Square Inner Product

var.xyz() var.pdbs()

Pairwise Distance Variance in Cartesian Coordinates

Correlation Network Analysis

Network analysis of protein structure and dynamic coupling

cna()

Protein Dynamic Correlation Network Construction and Community Analysis.

cnapath() summary(<cnapath>) print(<cnapath>) plot(<cnapath>) plot(<ecnapath>)

Suboptimal Path Analysis for Correlation Networks

dccm()

DCCM: Dynamical Cross-Correlation Matrix

filter.dccm()

Filter for Cross-correlation Matrices (Cij)

cmap()

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>) plot(<ecna>)

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

plotb3() plot(<bio3d>)

Plots with marginal SSE annotation

blast.pdb() get.blast() plot(<blast>)

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

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.scree>) plot(<pca.score>)

Plot PCA Results

plot(<pca.loadings>)

Plot Residue Loadings along PC1 to PC3

hclustplot()

Dendrogram with Clustering Annotation

plot(<cna>) plot(<ecna>)

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()

Convert to PDB format

as.select()

Convert Atomic Indices to a Select Object

is.xyz() as.xyz()

Is an Object of Class ‘xyz’?

atom.select() 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()

Manipulate PDB File Names

bio3d-package

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

blast.pdb() get.blast() plot(<blast>)

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

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 ‘pdb(s)’?

is.select()

Is an Object of Class ‘select’?

is.mol2()

Is an Object of Class ‘mol2’?

lbio3d()

List all Functions in the bio3d Package

mask()

Mask a Subset of Atoms in a DCCM Object.

orient.pdb()

Orient a PDB Structure

pairwise()

Pair Indices

plotb3() plot(<bio3d>)

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

cnapath() summary(<cnapath>) print(<cnapath>) plot(<cnapath>) plot(<ecnapath>)

Suboptimal Path Analysis for Correlation Networks

nma(<pdbs>) print(<enma>)

Ensemble Normal Mode Analysis

geostas() amsm.xyz() print(<geostas>)

GeoStaS Domain Finder

read.mol2() print(<mol2>)

Read MOL2 File

nma(<pdb>) build.hessian() print(<nma>)

Normal Mode Analysis

pca(<xyz>) print(<pca>)

Principal Component Analysis

read.pdb() read.pdb2() print(<pdb>) summary(<pdb>)

Read PDB File

read.prmtop() print(<prmtop>)

Read AMBER Parameter/Topology files

rle2() print(<rle2>)

Run Length Encoding with Indices

dssp() stride() print(<sse>)

Secondary Structure Analysis with DSSP or STRIDE

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 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

kinesin transducin hivp

Bio3d Example Data