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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 )

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

2,809

Version

2.2-4

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Barry Grant

Last Published

December 12th, 2015

Functions in bio3d (2.2-4)

Atom Names/Types to Mass Converter

AAindex: Amino Acid Index Database

Convert an Aminoacid Sequence to AAIndex Values

Alignment to FASTA object

Atom Selection from PDB and PRMTOP Structure Objects

Convert Atomic Indices to a Select Object

Table of Relevant Amino Acids

DCCM: Dynamical Cross-Correlation Matrix

Bounds of a Numeric Vector

Convert Between Atom and xyz Indices

Inspect And Clean Up A PDB Object

Amino Acid Residues to Mass Converter

Convert to PDB format

Identification of Invariant Core Positions

Shannon Entropy Score

Concatenate Multiple PDB Objects

Convert Between 1-letter and 3-letter Aminoacid Codes

Check on Missing Utility Programs

Secondary Structure Analysis with DSSP or STRIDE

Is an Object of Class ‘xyz’?

Principal Component Analysis

Find Sequence Motifs.

Atom Names/Types

difference.vector

Difference Vector

deformation.nma

Deformation Analysis

Bio3d Example Data

Download PDB Coordinate Files

Sequence Consensus for an Alignment

Principal Component Analysis of an arrary of matrices

Suboptimal Path Analysis for Correlation Networks

inspect.connectivity

Check the Connectivity of Protein Structures

Index for the sdENM ff

Create a HTML Page For a Given Alignment

Obtain A SSE Object From An SSE Sequence Vector

Alignment Gap Summary

Is an Object of Class ‘select’?

Filter for Cross-correlation Matrices (Cij)

Calculate the Angle Between Three Atoms

Protein Dynamic Correlation Network Construction and Community Analysis.

Binding Site Residues

Renumber and Convert Between Various PDB formats

Write AMBER Binary netCDF files

Biological Units Construction

Is an Object of Class ‘pdb(s)’?

Dynamic Cross-Correlation from Principal Component Analysis

Structure-based Sequence Alignment with MUSTANG

Sequence Generation from a Bounds Vector

Radius of Gyration

Mapping from alignment positions to PDB atomic indices

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Protein Structure Network Plots in 2D and 3D.

Diagonal Indices of a Matrix

Align a PDB structure to an existing alignment

Dynamic Cross-Correlation from Normal Modes Analysis

Combine Atom Selections From PDB Structure

Store all-atom data from a PDB object

Atom Names/Types to Atomic Symbols Converter

GeoStaS Domain Finder

Project Data onto Principal Components

Bhattacharyya Coefficient

Mass-weighted Inner Product

Pairwise Distance Variance in Cartesian Coordinates

Manipulate PDB File Names

LMI: Linear Mutual Information Matrix

PDBs to PDB Converter

Get Customizable Annotations From PDB

Plot eNMA Results

Calculate Covariance Matrix from Normal Modes

Read CHARMM/X-PLOR/NAMD Binary DCD files

Distance Matrix Analysis

network.amendment

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

HMMER Sequence Search

Plot RMSIP Results

Trim a XYZ Object of Cartesian Coordinates.

Prune A cna Network Object

Extract The Aminoacid Sequence From A PDB Object

Read AMBER Coordinate files

Dendrogram with Clustering Annotation

Wrap Torsion Angle Data

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

Contact Map Consensus Filtering

PDB File Coordinate Superposition

Sequence Alignment of PDB Files

Cross-Correlation for Ensemble NMA (eNMA)

Calculate the Distances Between the Rows of Two Matrices

Find Possible PDB Chain Breaks

Covariance Overlap

Fetch UniProt Entry Data.

DCCM: Dynamical Cross-Correlation Matrix

ENM Force Field Loader

normalize.vector

Mass-Weighted Normalized Vector

Sequence Alignment with MUSCLE

Atomic RMS Fluctuations

Ensemble Normal Mode Analysis

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Orient a PDB Structure

Plot a Summary of HMMER Hit Statistics.

Identify Points in a CNA Protein Structure Network Plot

NMA Fluctuations

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

Score Residue Conservation At Each Position in an Alignment

Principal Component Analysis

SSE Backbone Hydrogen Bonding

Overlap analysis

filter.identity

Percent Identity Filter

Periodic Table of the Elements

Principal Component Analysis

Write PQR Format Coordinate File

Read Aligned Structure Data

Printing XYZ coordinates

Root Mean Square Deviation

Download FASTA Sequence Files

Summarize and Print Features of a cna Network Graph

Calculate Torsion/Dihedral Angles

Biological Structure Analysis

Printing Core Positions and Returning Indices

View CNA Protein Structure Network Community Output in VMD

Obtain An SSE Sequence Vector From A PDB Object

Plot a Multiple Sequence Alignment

List all Functions in the bio3d Package

Plot Geostas Results

Plot PCA Results

Combine Sequences by Rows Without Recycling

Plot Fluctuations

Run Length Encoding with Indices

Plot Core Fitting Progress

Read Coordinate Data from Amber or Charmm

Read FASTA formated Sequences

read.crd.charmm

Percent Identity

Plots with marginal SSE annotation

Setup for Running Bio3D Functions using Multiple CPU Cores

Root Mean Square Inner Product

Visualization of Dynamic Cross-Correlation

Plot NMA Results

Trim a PDB Object To A Subset of Atoms.

Sequence Alignment of Identical Protein Sequences

Printing Sequence Alignments

Filter or Trim a PDBs Object

Protein Structure Network Layout

Square Inner Product

Read Aligned Structure Data

Write PDB Format Coordinate File

Vector Field Visualization of Modes

Structure Alignment Of Two PDB Files

Add a Sequence to an Existing Alignmnet

Write FASTA Formated Sequences

PCA / NMA Atomic Displacement Trajectory

Replicate Per-residue Vector Values

Write PIR Formated Sequences

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

Chemical Formula to Mass Converter

Normal Mode Analysis

Download Pfam FASTA Sequence Alignment

Plot Distance Matrix

Plot Contact Matrix

Normal Mode Analysis

Principal Component Analysis

Read AMBER Parameter/Topology files

Coordinate Superposition

Read PQR output from pdcBD File

Read AMBER Binary netCDF files

VMD Color Palette