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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
Getting started with Bio3D
PDB structure manipulation and analysis with Bio3D
Beginning trajectory analysis with Bio3D
Enhanced methods for Normal Mode Analysis with Bio3D
Comparative sequence and structure analysis with Bio3D
Ensemble NMA of E.coli DHFR structures
Ensemble NMA across multiple species of DHFR
Protein structure network analysis with Bio3D
Introduction to Ensemble Difference Distance Matrix (eDDM) Analysis
Online protein structure analysis with the Bio3D WebApp ( PDF)
Online Normal Mode Analysis with Bio3D WebApps ( PDF | HTML )

There is also extensive on-line documentation with worked examples (and their output) for all functions and a package manual (in PDF format) that is a concatenation of each functions documentation (without example output).

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

2.4-4

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Last Published

October 26th, 2022

Functions in bio3d (2.4-4)

Amino Acid Residues to Mass Converter

All Atom Normal Mode Analysis

Ensemble Normal Mode Analysis with All-Atom ENM

Convert Between 1-letter and 3-letter Aminoacid Codes

Calculate the Angle Between Three Atoms

Table of Relevant Amino Acids

Convert an Aminoacid Sequence to AAIndex Values

AAindex: Amino Acid Index Database

Create a HTML Page For a Given Alignment

Alignment to FASTA object

Atom Names/Types to Atomic Symbols Converter

Manipulate PDB File Names

Atom Selection from PDB and PRMTOP Structure Objects

Bhattacharyya Coefficient

Binding Site Residues

Atom Names/Types

Convert Atomic Indices to a Select Object

Convert Between Atom and xyz Indices

Atom Names/Types to Mass Converter

Convert to PDB format

Biological Structure Analysis

Obtain A SSE Object From An SSE Sequence Vector

Concatenate Multiple PDB Objects

Inspect And Clean Up A PDB Object

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

Check on Missing Utility Programs

Find Possible PDB Chain Breaks

Bounds of a Numeric Vector

Biological Units Construction

Protein Dynamic Correlation Network Construction and Community Analysis.

Suboptimal Path Analysis for Correlation Networks

Score Residue Conservation At Each Position in an Alignment

Align communities from two or more networks

Combine Atom Selections From PDB Structure

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

Renumber and Convert Between Various PDB formats

Sequence Consensus for an Alignment

Cross-Correlation for Ensemble NMA (eNMA)

Covariance Overlap

Dynamic Cross-Correlation from Normal Modes Analysis

DCCM: Dynamical Cross-Correlation Matrix

Identification of Contact Map Core Positions

Calculate Covariance Matrix from Normal Modes

Dynamical Cross-Correlation Matrix from Cartesian Coordinates

Identification of Invariant Core Positions

Dynamic Cross-Correlation from Gaussian Network Model

Periodic Table of the Elements

Diagonal Indices of a Matrix

deformation.nma

Deformation Analysis

Dynamical Cross-Correlation Matrix from Principal Component Analysis

Shannon Entropy Score

difference.vector

Difference Vector

Calculate the Distances Between the Rows of Two Matrices

Contact Map Consensus Filtering

Distance Matrix Analysis

Bio3d Example Data

Download FASTA Sequence Files

Download PDB Coordinate Files

Alignment Gap Summary

GeoStaS Domain Finder

Filter for Cross-correlation Matrices (Cij)

Coordinate Superposition

filter.identity

Percent Identity Filter

Secondary Structure Analysis with DSSP or STRIDE

NMA Fluctuations

Is an Object of Class ‘select’?

Identify Points in a CNA Protein Structure Network Plot

Chemical Formula to Mass Converter

Is an Object of Class ‘pdb(s)’?

HMMER Sequence Search

Gaussian Network Model

Dendrogram with Clustering Annotation

network.amendment

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

Structure-based Sequence Alignment with MUSTANG

Is an Object of Class ‘mol2’?

Find Sequence Motifs.

inspect.connectivity

Check the Connectivity of Protein Structures

Is an Object of Class ‘xyz’?

Mass-weighted Inner Product

Protein Structure Network Layout

Mask a Subset of Atoms in a DCCM Object.

Principal Component Analysis

Normal Mode Analysis

Ensemble Normal Mode Analysis

Normal Mode Analysis

Principal Component Analysis

Orient a PDB Structure

PCA / NMA Atomic Displacement Trajectory

normalize.vector

Mass-Weighted Normalized Vector

Extract The Aminoacid Sequence From A PDB Object

Overlap analysis

Obtain An SSE Sequence Vector From A PDB Object

Principal Component Analysis of an array of matrices

SSE annotation for a PDBs Object

List all Functions in the bio3d Package

ENM Force Field Loader

Sequence Alignment of PDB Files

Principal Component Analysis

Get Customizable Annotations From PDB Or PFAM Databases

Principal Component Analysis

PDBs to PDB Converter

PDB File Coordinate Superposition

Plot a Multiple Sequence Alignment

Plot eNMA Results

Align a PDB structure to an existing alignment

Protein Structure Network Plots in 2D and 3D.

Plots with marginal SSE annotation

Mapping from alignment positions to PDB atomic indices

Plot Core Fitting Progress

Plot Distance Matrix

Plot Contact Matrix

Download Pfam FASTA Sequence Alignment

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

Plot Fluctuations

Plot a Summary of HMMER Hit Statistics.

Printing Core Positions and Returning Indices

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Plot NMA Results

plot.matrix.loadings

Plot Residue-Residue Matrix Loadings

Summarize and Print Features of a cna Network Graph

Plot RMSIP Results

Plot PCA Results

Plot Geostas Results

Read mmCIF File

read.crd.charmm

Read AMBER Coordinate files

Read Coordinate Data from Amber or Charmm

Prune A cna Network Object

Biomolecular Visualization with PyMOL

Project Data onto Principal Components

Printing Sequence Alignments

Read FASTA formated Sequences

Read Aligned Structure Data

Read Aligned Structure Data

Printing XYZ coordinates

Radius of Gyration

Read AMBER Parameter/Topology files

Read AMBER Binary netCDF files

Read CHARMM/X-PLOR/NAMD Binary DCD files

Read PQR output from pdcBD File

Index for the sdENM ff

Add a Sequence to an Existing Alignmnet

Combine Sequences by Rows Without Recycling

Percent Identity

Atomic RMS Fluctuations

Root Mean Square Inner Product

Root Mean Square Deviation

Run Length Encoding with Indices

Setup for Running Bio3D Functions using Multiple CPU Cores

Trim a PDB Object To A Subset of Atoms.

Filter or Trim a PDBs Object

Square Inner Product

Calculate Torsion/Dihedral Angles

Store all-atom data from a PDB object

Trim a MOL2 Object To A Subset of Atoms.

Replicate Per-residue Vector Values

Sequence Alignment of Identical Protein Sequences

Sequence Alignment with MUSCLE

Pairwise Distance Variance in Cartesian Coordinates

Sequence Generation from a Bounds Vector

Fetch UniProt Entry Data.

SSE Backbone Hydrogen Bonding

Trim a XYZ Object of Cartesian Coordinates.

View CNA Protein Structure Network Community Output in VMD

Write PDB Format Coordinate File

Write AMBER Binary netCDF files

Write MOL2 Format Coordinate File

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Structure Alignment Of Two PDB Files

Write FASTA Formated Sequences

VMD Color Palette

Wrap Torsion Angle Data

Write PQR Format Coordinate File

Write PIR Formated Sequences