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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

2,276

Version

2.4-1

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Barry Grant

Last Published

January 21st, 2020

Functions in bio3d (2.4-1)

Create a HTML Page For a Given Alignment

Atom Names/Types

Atom Selection from PDB and PRMTOP Structure Objects

Bhattacharyya Coefficient

Binding Site Residues

Convert to PDB format

Manipulate PDB File Names

Convert Atomic Indices to a Select Object

Convert Between Atom and xyz Indices

Concatenate Multiple PDB Objects

Check on Missing Utility Programs

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

Find Possible PDB Chain Breaks

Bounds of a Numeric Vector

Inspect And Clean Up A PDB Object

Combine Atom Selections From PDB Structure

Align communities from two or more networks

Obtain A SSE Object From An SSE Sequence Vector

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

Cross-Correlation for Ensemble NMA (eNMA)

DCCM: Dynamical Cross-Correlation Matrix

Suboptimal Path Analysis for Correlation Networks

Covariance Overlap

Calculate Covariance Matrix from Normal Modes

Sequence Consensus for an Alignment

Score Residue Conservation At Each Position in an Alignment

Dynamic Cross-Correlation from Normal Modes Analysis

Dynamic Cross-Correlation from Gaussian Network Model

Atom Names/Types to Atomic Symbols Converter

Dynamical Cross-Correlation Matrix from Principal Component Analysis

Biological Structure Analysis

Biological Units Construction

Atom Names/Types to Mass Converter

Protein Dynamic Correlation Network Construction and Community Analysis.

Renumber and Convert Between Various PDB formats

Identification of Invariant Core Positions

Identification of Contact Map Core Positions

Bio3d Example Data

Contact Map Consensus Filtering

Dynamical Cross-Correlation Matrix from Cartesian Coordinates

Secondary Structure Analysis with DSSP or STRIDE

Distance Matrix Analysis

Periodic Table of the Elements

Shannon Entropy Score

NMA Fluctuations

difference.vector

Difference Vector

Chemical Formula to Mass Converter

Coordinate Superposition

Download PDB Coordinate Files

Calculate the Distances Between the Rows of Two Matrices

Download FASTA Sequence Files

Diagonal Indices of a Matrix

deformation.nma

Deformation Analysis

Filter for Cross-correlation Matrices (Cij)

Is an Object of Class ‘select’?

Is an Object of Class ‘pdb(s)’?

Find Sequence Motifs.

Structure-based Sequence Alignment with MUSTANG

Orient a PDB Structure

normalize.vector

Mass-Weighted Normalized Vector

SSE annotation for a PDBs Object

Gaussian Network Model

Dendrogram with Clustering Annotation

filter.identity

Percent Identity Filter

Alignment Gap Summary

GeoStaS Domain Finder

Extract The Aminoacid Sequence From A PDB Object

HMMER Sequence Search

List all Functions in the bio3d Package

Identify Points in a CNA Protein Structure Network Plot

Overlap analysis

ENM Force Field Loader

network.amendment

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

Mass-weighted Inner Product

Plot eNMA Results

inspect.connectivity

Check the Connectivity of Protein Structures

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.

Normal Mode Analysis

Download Pfam FASTA Sequence Alignment

Plot a Summary of HMMER Hit Statistics.

Principal Component Analysis

Printing Core Positions and Returning Indices

Summarize and Print Features of a cna Network Graph

Read AMBER Coordinate files

read.crd.charmm

Plot a Multiple Sequence Alignment

Get Customizable Annotations From PDB Or PFAM Databases

Principal Component Analysis of an array of matrices

Principal Component Analysis

Plots with marginal SSE annotation

plot.matrix.loadings

Plot Residue-Residue Matrix Loadings

Project Data onto Principal Components

Prune A cna Network Object

Read CHARMM/X-PLOR/NAMD Binary DCD files

Read Aligned Structure Data

Plot Fluctuations

Plot Contact Matrix

Plot Geostas Results

Printing Sequence Alignments

Printing XYZ coordinates

Read AMBER Binary netCDF files

Percent Identity

Combine Sequences by Rows Without Recycling

Run Length Encoding with Indices

Read FASTA formated Sequences

SSE Backbone Hydrogen Bonding

Root Mean Square Deviation

Filter or Trim a PDBs Object

Index for the sdENM ff

Trim a PDB Object To A Subset of Atoms.

Write FASTA Formated Sequences

Add a Sequence to an Existing Alignmnet

PCA / NMA Atomic Displacement Trajectory

Mask a Subset of Atoms in a DCCM Object.

Principal Component Analysis

Principal Component Analysis

Obtain An SSE Sequence Vector From A PDB Object

Sequence Alignment of PDB Files

Structure Alignment Of Two PDB Files

Is an Object of Class ‘mol2’?

Store all-atom data from a PDB object

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Trim a XYZ Object of Cartesian Coordinates.

Sequence Generation from a Bounds Vector

Fetch UniProt Entry Data.

Write PQR Format Coordinate File

Is an Object of Class ‘xyz’?

Protein Structure Network Plots in 2D and 3D.

PDB File Coordinate Superposition

PDBs to PDB Converter

Plot Core Fitting Progress

Pairwise Distance Variance in Cartesian Coordinates

Normal Mode Analysis

Protein Structure Network Layout

Ensemble Normal Mode Analysis

Plot Distance Matrix

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Plot RMSIP Results

Read mmCIF File

Plot NMA Results

Biomolecular Visualization with PyMOL

Plot PCA Results

Read PQR output from pdcBD File

Read Aligned Structure Data

Read AMBER Parameter/Topology files

Sequence Alignment of Identical Protein Sequences

Read Coordinate Data from Amber or Charmm

Calculate Torsion/Dihedral Angles

Radius of Gyration

Sequence Alignment with MUSCLE

Atomic RMS Fluctuations

VMD Color Palette

Trim a MOL2 Object To A Subset of Atoms.

Wrap Torsion Angle Data

Setup for Running Bio3D Functions using Multiple CPU Cores

Root Mean Square Inner Product

Square Inner Product

Write PDB Format Coordinate File

Replicate Per-residue Vector Values

Write PIR Formated Sequences

View CNA Protein Structure Network Community Output in VMD

Write AMBER Binary netCDF files

Write MOL2 Format Coordinate File

Ensemble Normal Mode Analysis with All-Atom ENM

Calculate the Angle Between Three Atoms

Table of Relevant Amino Acids

Convert Between 1-letter and 3-letter Aminoacid Codes

Convert an Aminoacid Sequence to AAIndex Values

Amino Acid Residues to Mass Converter

Alignment to FASTA object

AAindex: Amino Acid Index Database

All Atom Normal Mode Analysis