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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
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

4,789

Version

2.4-3

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Barry Grant

Last Published

March 10th, 2022

Functions in bio3d (2.4-3)

Alignment to FASTA object

All Atom Normal Mode Analysis

Table of Relevant Amino Acids

AAindex: Amino Acid Index Database

Calculate the Angle Between Three Atoms

Amino Acid Residues to Mass Converter

Ensemble Normal Mode Analysis with All-Atom ENM

Create a HTML Page For a Given Alignment

Convert an Aminoacid Sequence to AAIndex Values

Convert Between 1-letter and 3-letter Aminoacid Codes

Bhattacharyya Coefficient

Manipulate PDB File Names

Convert Between Atom and xyz Indices

Binding Site Residues

Biological Units Construction

Biological Structure Analysis

Obtain A SSE Object From An SSE Sequence Vector

Convert Atomic Indices to a Select Object

Bounds of a Numeric Vector

Convert to PDB format

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

Score Residue Conservation At Each Position in an Alignment

Renumber and Convert Between Various PDB formats

Inspect And Clean Up A PDB Object

Atom Names/Types

Atom Selection from PDB and PRMTOP Structure Objects

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

Check on Missing Utility Programs

Combine Atom Selections From PDB Structure

DCCM: Dynamical Cross-Correlation Matrix

Sequence Consensus for an Alignment

Atom Names/Types to Atomic Symbols Converter

Atom Names/Types to Mass Converter

Cross-Correlation for Ensemble NMA (eNMA)

Periodic Table of the Elements

Shannon Entropy Score

Distance Matrix Analysis

Secondary Structure Analysis with DSSP or STRIDE

Covariance Overlap

Bio3d Example Data

Calculate Covariance Matrix from Normal Modes

Protein Dynamic Correlation Network Construction and Community Analysis.

Coordinate Superposition

Contact Map Consensus Filtering

Normal Mode Analysis

network.amendment

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

Concatenate Multiple PDB Objects

Chemical Formula to Mass Converter

Identify Points in a CNA Protein Structure Network Plot

HMMER Sequence Search

NMA Fluctuations

Mask a Subset of Atoms in a DCCM Object.

Download PDB Coordinate Files

PCA / NMA Atomic Displacement Trajectory

Normal Mode Analysis

Align communities from two or more networks

PDB File Coordinate Superposition

Find Possible PDB Chain Breaks

Identification of Invariant Core Positions

Identification of Contact Map Core Positions

Dynamic Cross-Correlation from Gaussian Network Model

Alignment Gap Summary

difference.vector

Difference Vector

Mass-weighted Inner Product

GeoStaS Domain Finder

Calculate the Distances Between the Rows of Two Matrices

Ensemble Normal Mode Analysis

normalize.vector

Mass-Weighted Normalized Vector

Orient a PDB Structure

inspect.connectivity

Check the Connectivity of Protein Structures

Plot Distance Matrix

Is an Object of Class ‘pdb(s)’?

List all Functions in the bio3d Package

Is an Object of Class ‘select’?

Download FASTA Sequence Files

Align a PDB structure to an existing alignment

Dynamic Cross-Correlation from Normal Modes Analysis

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Biomolecular Visualization with PyMOL

Is an Object of Class ‘xyz’?

Gaussian Network Model

Filter for Cross-correlation Matrices (Cij)

Read Aligned Structure Data

PDBs to PDB Converter

Plot eNMA Results

filter.identity

Percent Identity Filter

Mapping from alignment positions to PDB atomic indices

Dendrogram with Clustering Annotation

Plot RMSIP Results

ENM Force Field Loader

Plot a Multiple Sequence Alignment

Read AMBER Parameter/Topology files

Printing Sequence Alignments

Printing XYZ coordinates

Overlap analysis

Radius of Gyration

Obtain An SSE Sequence Vector From A PDB Object

Plots with marginal SSE annotation

Sequence Alignment of PDB Files

Suboptimal Path Analysis for Correlation Networks

Plot Core Fitting Progress

Run Length Encoding with Indices

Protein Structure Network Plots in 2D and 3D.

Plot PCA Results

Plot NMA Results

Dynamical Cross-Correlation Matrix from Principal Component Analysis

Sequence Generation from a Bounds Vector

Prune A cna Network Object

Structure Alignment Of Two PDB Files

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Root Mean Square Deviation

Trim a XYZ Object of Cartesian Coordinates.

Read CHARMM/X-PLOR/NAMD Binary DCD files

Project Data onto Principal Components

Read PQR output from pdcBD File

Write PQR Format Coordinate File

Read FASTA formated Sequences

Plot Fluctuations

Plot Contact Matrix

Read AMBER Coordinate files

Plot Geostas Results

SSE Backbone Hydrogen Bonding

Atomic RMS Fluctuations

Store all-atom data from a PDB object

Combine Sequences by Rows Without Recycling

Root Mean Square Inner Product

read.crd.charmm

Read Aligned Structure Data

Percent Identity

Protein Structure Network Layout

deformation.nma

Deformation Analysis

Find Sequence Motifs.

Replicate Per-residue Vector Values

Diagonal Indices of a Matrix

View CNA Protein Structure Network Community Output in VMD

Is an Object of Class ‘mol2’?

Dynamical Cross-Correlation Matrix from Cartesian Coordinates

Principal Component Analysis

Principal Component Analysis

Structure-based Sequence Alignment with MUSTANG

Index for the sdENM ff

Principal Component Analysis

Principal Component Analysis of an array of matrices

Extract The Aminoacid Sequence From A PDB Object

Principal Component Analysis

Get Customizable Annotations From PDB Or PFAM Databases

SSE annotation for a PDBs Object

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

plot.matrix.loadings

Plot Residue-Residue Matrix Loadings

Plot a Summary of HMMER Hit Statistics.

Read mmCIF File

Sequence Alignment of Identical Protein Sequences

Write MOL2 Format Coordinate File

Calculate Torsion/Dihedral Angles

Read Coordinate Data from Amber or Charmm

Write AMBER Binary netCDF files

Trim a MOL2 Object To A Subset of Atoms.

Sequence Alignment with MUSCLE

Setup for Running Bio3D Functions using Multiple CPU Cores

Summarize and Print Features of a cna Network Graph

Download Pfam FASTA Sequence Alignment

Printing Core Positions and Returning Indices

Wrap Torsion Angle Data

VMD Color Palette

Square Inner Product

Trim a PDB Object To A Subset of Atoms.

Read AMBER Binary netCDF files

Add a Sequence to an Existing Alignmnet

Filter or Trim a PDBs Object

Pairwise Distance Variance in Cartesian Coordinates

Fetch UniProt Entry Data.

Write PDB Format Coordinate File

Write PIR Formated Sequences

Write FASTA Formated Sequences