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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

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Version

Install

install.packages('bio3d')

Monthly Downloads

2,628

Version

2.3-3

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Barry Grant

Last Published

July 31st, 2017

Functions in bio3d (2.3-3)

Calculate the Angle Between Three Atoms

Alignment to FASTA object

Convert Between 1-letter and 3-letter Aminoacid Codes

Convert an Aminoacid Sequence to AAIndex Values

AAindex: Amino Acid Index Database

Table of Relevant Amino Acids

Ensemble Normal Mode Analysis with All-Atom ENM

Create a HTML Page For a Given Alignment

Amino Acid Residues to Mass Converter

All Atom Normal Mode Analysis

Atom Names/Types

Atom Selection from PDB and PRMTOP Structure Objects

Atom Names/Types to Atomic Symbols Converter

Atom Names/Types to Mass Converter

Biological Structure Analysis

Biological Units Construction

Score Residue Conservation At Each Position in an Alignment

Renumber and Convert Between Various PDB formats

DCCM: Dynamical Cross-Correlation Matrix

deformation.nma

Deformation Analysis

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

Bounds of a Numeric Vector

Combine Atom Selections From PDB Structure

Align communities from two or more networks

Identification of Invariant Core Positions

Calculate Covariance Matrix from Normal Modes

Bhattacharyya Coefficient

Binding Site Residues

Obtain A SSE Object From An SSE Sequence Vector

Convert to PDB format

Convert Atomic Indices to a Select Object

Check on Missing Utility Programs

Inspect And Clean Up A PDB Object

Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object.

Sequence Consensus for an Alignment

Covariance Overlap

DCCM: Dynamical Cross-Correlation Matrix

Suboptimal Path Analysis for Correlation Networks

Dynamic Cross-Correlation from Normal Modes Analysis

Dynamic Cross-Correlation from Principal Component Analysis

Contact Map Consensus Filtering

Filter for Cross-correlation Matrices (Cij)

GeoStaS Domain Finder

Download PDB Coordinate Files

Diagonal Indices of a Matrix

difference.vector

Difference Vector

filter.identity

Percent Identity Filter

Convert Between Atom and xyz Indices

Manipulate PDB File Names

Concatenate Multiple PDB Objects

Find Possible PDB Chain Breaks

Shannon Entropy Score

Bio3d Example Data

Coordinate Superposition

NMA Fluctuations

Is an Object of Class ‘mol2’?

Is an Object of Class ‘pdb(s)’?

Find Sequence Motifs.

Structure-based Sequence Alignment with MUSTANG

Identify Points in a CNA Protein Structure Network Plot

Mass-weighted Inner Product

Mask a Subset of Atoms in a DCCM Object.

Protein Dynamic Correlation Network Construction and Community Analysis.

Cross-Correlation for Ensemble NMA (eNMA)

Dynamic Cross-Correlation from Gaussian Network Model

PCA / NMA Atomic Displacement Trajectory

Principal Component Analysis

Principal Component Analysis

Normal Mode Analysis

Ensemble Normal Mode Analysis

Align a PDB structure to an existing alignment

Mapping from alignment positions to PDB atomic indices

Split a PDB File Into Separate Files, One For Each Chain.

Download Pfam FASTA Sequence Alignment

Summarize and Print Features of a cna Network Graph

Printing Core Positions and Returning Indices

Calculate the Distances Between the Rows of Two Matrices

Distance Matrix Analysis

Chemical Formula to Mass Converter

Alignment Gap Summary

PDB File Coordinate Superposition

PDBs to PDB Converter

Plots with marginal SSE annotation

Plot Contact Matrix

inspect.connectivity

Check the Connectivity of Protein Structures

Protein Structure Network Layout

List all Functions in the bio3d Package

Is an Object of Class ‘xyz’?

network.amendment

Amendment of a CNA Network According To A Input Community Membership Vector.

Normal Mode Analysis

Secondary Structure Analysis with DSSP or STRIDE

Periodic Table of the Elements

Download FASTA Sequence Files

Gaussian Network Model

Is an Object of Class ‘select’?

Dendrogram with Clustering Annotation

HMMER Sequence Search

LMI: Linear Mutual Information Matrix

ENM Force Field Loader

Read AMBER Coordinate files

read.crd.charmm

Read AMBER Binary netCDF files

Overlap analysis

Principal Component Analysis

Get Customizable Annotations From PDB Or PFAM Databases

Plot Distance Matrix

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Sequence Alignment with MUSCLE

Sequence Alignment of Identical Protein Sequences

Trim a PDB Object To A Subset of Atoms.

Filter or Trim a PDBs Object

Plot Fluctuations

Plot Geostas Results

Biomolecular Visualization with PyMOL

Read Aligned Structure Data

Read AMBER Parameter/Topology files

Radius of Gyration

Atomic RMS Fluctuations

Root Mean Square Inner Product

SSE Backbone Hydrogen Bonding

Store all-atom data from a PDB object

normalize.vector

Mass-Weighted Normalized Vector

Orient a PDB Structure

SSE annotation for a PDBs Object

Extract The Aminoacid Sequence From A PDB Object

Write FASTA Formated Sequences

Write PQR Format Coordinate File

Principal Component Analysis

Principal Component Analysis of an array of matrices

Obtain An SSE Sequence Vector From A PDB Object

Sequence Alignment of PDB Files

Plot RMSIP Results

Project Data onto Principal Components

Prune A cna Network Object

Read CHARMM/X-PLOR/NAMD Binary DCD files

Fetch UniProt Entry Data.

Pairwise Distance Variance in Cartesian Coordinates

Plot eNMA Results

Plot a Multiple Sequence Alignment

Plot a Summary of HMMER Hit Statistics.

plot.matrix.loadings

Plot Residue-Residue Matrix Loadings

Read mmCIF File

Protein Structure Network Plots in 2D and 3D.

Plot Core Fitting Progress

Plot NMA Results

Plot PCA Results

Read Coordinate Data from Amber or Charmm

Read PQR output from pdcBD File

Combine Sequences by Rows Without Recycling

Percent Identity

Calculate Torsion/Dihedral Angles

Printing Sequence Alignments

Printing XYZ coordinates

Read Aligned Structure Data

Run Length Encoding with Indices

Root Mean Square Deviation

Setup for Running Bio3D Functions using Multiple CPU Cores

Trim a MOL2 Object To A Subset of Atoms.

VMD Color Palette

Wrap Torsion Angle Data

Read FASTA formated Sequences

Index for the sdENM ff

Add a Sequence to an Existing Alignmnet

Structure Alignment Of Two PDB Files

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Replicate Per-residue Vector Values

View CNA Protein Structure Network Community Output in VMD

Square Inner Product

Trim a XYZ Object of Cartesian Coordinates.

Sequence Generation from a Bounds Vector

Write MOL2 Format Coordinate File

Write AMBER Binary netCDF files

Write PDB Format Coordinate File

Write PIR Formated Sequences