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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

1,824

Version

2.3-4

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Last Published

April 3rd, 2018

Functions in bio3d (2.3-4)

Biological Structure Analysis

Obtain A SSE Object From An SSE Sequence Vector

Atom Names/Types to Mass Converter

DCCM: Dynamical Cross-Correlation Matrix

Align communities from two or more networks

Diagonal Indices of a Matrix

deformation.nma

Deformation Analysis

Chemical Formula to Mass Converter

Concatenate Multiple PDB Objects

Combine Atom Selections From PDB Structure

Contact Map Consensus Filtering

difference.vector

Difference Vector

Find Possible PDB Chain Breaks

Coordinate Superposition

Calculate Covariance Matrix from Normal Modes

Suboptimal Path Analysis for Correlation Networks

Identification of Invariant Core Positions

Filter for Cross-correlation Matrices (Cij)

Biological Units Construction

NMA Fluctuations

Bounds of a Numeric Vector

DCCM: Dynamical Cross-Correlation Matrix

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

Covariance Overlap

Renumber and Convert Between Various PDB formats

Alignment Gap Summary

Score Residue Conservation At Each Position in an Alignment

Inspect And Clean Up A PDB Object

Is an Object of Class ‘select’?

Identify Points in a CNA Protein Structure Network Plot

network.amendment

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

Is an Object of Class ‘xyz’?

Protein Dynamic Correlation Network Construction and Community Analysis.

Normal Mode Analysis

Principal Component Analysis

Check on Missing Utility Programs

Cross-Correlation for Ensemble NMA (eNMA)

Shannon Entropy Score

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

Dynamic Cross-Correlation from Gaussian Network Model

Sequence Consensus for an Alignment

Distance Matrix Analysis

Bio3d Example Data

Calculate the Distances Between the Rows of Two Matrices

GeoStaS Domain Finder

Download PDB Coordinate Files

Gaussian Network Model

Principal Component Analysis

Mass-weighted Inner Product

Download FASTA Sequence Files

Structure-based Sequence Alignment with MUSTANG

Find Sequence Motifs.

Dendrogram with Clustering Annotation

Overlap analysis

HMMER Sequence Search

SSE annotation for a PDBs Object

PDB File Coordinate Superposition

Mask a Subset of Atoms in a DCCM Object.

PDBs to PDB Converter

inspect.connectivity

Check the Connectivity of Protein Structures

Dynamic Cross-Correlation from Normal Modes Analysis

Dynamic Cross-Correlation from Principal Component Analysis

PCA / NMA Atomic Displacement Trajectory

Extract The Aminoacid Sequence From A PDB Object

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

Plots with marginal SSE annotation

Normal Mode Analysis

Secondary Structure Analysis with DSSP or STRIDE

Plot Contact Matrix

Obtain An SSE Sequence Vector From A PDB Object

Download Pfam FASTA Sequence Alignment

Ensemble Normal Mode Analysis

plot.matrix.loadings

Plot Residue-Residue Matrix Loadings

Plot a Summary of HMMER Hit Statistics.

Periodic Table of the Elements

Plot NMA Results

Printing Sequence Alignments

Plot PCA Results

Project Data onto Principal Components

Sequence Alignment of PDB Files

Protein Structure Network Layout

normalize.vector

Mass-Weighted Normalized Vector

List all Functions in the bio3d Package

Read AMBER Parameter/Topology files

Plot eNMA Results

Printing XYZ coordinates

Radius of Gyration

Prune A cna Network Object

Read Aligned Structure Data

Orient a PDB Structure

Sequence Alignment with MUSCLE

Sequence Alignment of Identical Protein Sequences

Structure Alignment Of Two PDB Files

Align a PDB structure to an existing alignment

filter.identity

Percent Identity Filter

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Plot a Multiple Sequence Alignment

Summarize and Print Features of a cna Network Graph

Is an Object of Class ‘mol2’?

LMI: Linear Mutual Information Matrix

Write FASTA Formated Sequences

Is an Object of Class ‘pdb(s)’?

Mapping from alignment positions to PDB atomic indices

Printing Core Positions and Returning Indices

Atomic RMS Fluctuations

Protein Structure Network Plots in 2D and 3D.

ENM Force Field Loader

Principal Component Analysis

Principal Component Analysis

Principal Component Analysis of an array of matrices

Get Customizable Annotations From PDB Or PFAM Databases

Plot Core Fitting Progress

Read AMBER Coordinate files

Root Mean Square Inner Product

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Plot RMSIP Results

Read mmCIF File

Read Coordinate Data from Amber or Charmm

Trim a MOL2 Object To A Subset of Atoms.

read.crd.charmm

Calculate Torsion/Dihedral Angles

Fetch UniProt Entry Data.

Read AMBER Binary netCDF files

Read PQR output from pdcBD File

Plot Distance Matrix

Plot Fluctuations

Pairwise Distance Variance in Cartesian Coordinates

Plot Geostas Results

Biomolecular Visualization with PyMOL

Combine Sequences by Rows Without Recycling

Index for the sdENM ff

Read Aligned Structure Data

Read CHARMM/X-PLOR/NAMD Binary DCD files

Read FASTA formated Sequences

Add a Sequence to an Existing Alignmnet

Trim a PDB Object To A Subset of Atoms.

Run Length Encoding with Indices

Percent Identity

SSE Backbone Hydrogen Bonding

Root Mean Square Deviation

Store all-atom data from a PDB object

Replicate Per-residue Vector Values

Filter or Trim a PDBs Object

View CNA Protein Structure Network Community Output in VMD

Write PDB Format Coordinate File

Write PIR Formated Sequences

Trim a XYZ Object of Cartesian Coordinates.

Setup for Running Bio3D Functions using Multiple CPU Cores

Square Inner Product

Sequence Generation from a Bounds Vector

VMD Color Palette

Wrap Torsion Angle Data

Write PQR Format Coordinate File

Write MOL2 Format Coordinate File

Write AMBER Binary netCDF files

Ensemble Normal Mode Analysis with All-Atom ENM

Convert Between 1-letter and 3-letter Aminoacid Codes

Amino Acid Residues to Mass Converter

All Atom Normal Mode Analysis

Create a HTML Page For a Given Alignment

Convert an Aminoacid Sequence to AAIndex Values

Calculate the Angle Between Three Atoms

Table of Relevant Amino Acids

Alignment to FASTA object

AAindex: Amino Acid Index Database

Bhattacharyya Coefficient

Convert to PDB format

Manipulate PDB File Names

Atom Names/Types

Atom Names/Types to Atomic Symbols Converter

Convert Between Atom and xyz Indices

Convert Atomic Indices to a Select Object

Atom Selection from PDB and PRMTOP Structure Objects

Binding Site Residues