Learn R Programming

⚠️There's a newer version (2.4-4) of this package.Take me there.

bio3d (version 2.1-1)

Biological Structure Analysis

Description

Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.

Copy Link

Version

Install

install.packages('bio3d')

Monthly Downloads

2,628

Version

2.1-1

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Barry Grant

Last Published

October 15th, 2014

Functions in bio3d (2.1-1)

Dynamic Cross-Correlation from Principal Component Analysis

DCCM: Dynamical Cross-Correlation Matrix

Check on Missing Utility Programs

Download PDB Coordinate Files

PCA Atomic Displacement Trajectory

Normal Mode Analysis

Identification of Invariant Core Positions

Ensemble Normal Mode Analysis

Biological Structure Analysis

Coordinate Superposition

Secondary Structure Analysis with DSSP or STRIDE

Get Customizable Annotations From PDB

Principal Component Analysis

Chemical Formula to Mass Converter

ENM Force Field Loader

Periodic Table of the Elements

Renumber and Convert Between Various PDB formats

Sequence Alignment with MUSCLE

Bhattacharyya Coefficient

Normal Mode Analysis

Covariance Overlap

Calculate Covariance Matrix from Normal Modes

Download Pfam FASTA Sequence Alignment

Score Residue Conservation At Each Position in an Alignment

Align a PDB structure to an existing alignment

NMA Fluctuations

Atom Names/Types to Atomic Symbols Converter

Write FASTA Formated Sequences

Atom Names/Types

LMI: Linear Mutual Information Matrix

Principal Component Analysis

Protein Dynamic Correlation Network Construction and Community Analysis.

Plot a Multiple Sequence Alignment

Plot Distance Matrix

Bio3d Example Data

Read Aligned Structure Data

Plot PCA Results

Plot a Summary of BLAST Hit Statistics.

deformation.nma

Deformation Analysis

normalize.vector

Mass-Weighted Normalized Vector

Write PDB Format Coordinate File

Read CHARMM/X-PLOR/NAMD Binary DCD files

List all Functions in the bio3d Package

Root Mean Square Inner Product

Plot NMA Results

Principal Component Analysis

Convert an Aminoacid Sequence to AAIndex Values

PDB File Coordinate Superposition

Alignment Gap Summary

Shannon Entropy Score

Distance Matrix Analysis

Bounds of a Numeric Vector

Write PQR Format Coordinate File

Convert Between 1-letter and 3-letter Aminoacid Codes

Ensemble NMA Atomic Displacement Trajectory

Cross-Correlation for Ensemble NMA (eNMA)

Atom Names/Types to Mass Converter

Is an Object of Class pdb(s)?

Mass-weighted Inner Product

Plot RMSIP Results

Identify Points in a CNA Protein Structure Network Plot

Convert Between Atom and xyz Indices

Filter or Trim a pdbs PDBs Object

Filter for Cross-correlation Matrices (Cij)

Overlap analysis

Amino Acid Residues to Mass Converter

Pairwise Distance Variance in Cartesian Coordinates

Atomic RMS Fluctuations

Binding Site Residues

Contact Map Consensus Filtering

Secondary Structure Analysis of Aligned PDB Structures with DSSP

DCCM: Dynamical Cross-Correlation Matrix

Dynamic Cross-Correlation from Normal Modes Analysis

Secondary Structure Analysis of Trajectories with DSSP

Read FASTA formated Sequences

Sequence Alignment of Identical Protein Sequences

Extract The Aminoacid Sequence From A PDB Object

inspect.connectivity

Check the Connectivity of Protein Structures

Index for the sdENM ff

Principal Component Analysis of an arrary of matrices

Write AMBER Binary netCDF files

Setup for Running Bio3D Functions using Multiple CPU Cores

Calculate Torsion/Dihedral Angles

Combine Sequences by Rows Without Recycling

Diagonal Indices of a Matrix

Protein Structure Network Plots in 2D and 3D.

Read Aligned Structure Data

Replicate Per-residue Vector Values

Structure-based Sequence Alignment with MUSTANG

Plot eNMA Results

Find Possible PDB Chain Breaks

Percent Identity

Printing XYZ coordinates

Plots with marginal SSE annotation

difference.vector

Difference Vector

Structure Alignment Of Two PDB Files

Mapping between PDB atomic indices and alignment positions

Project Data onto Principal Components

Sequence Generation from a Bounds Vector

Sequence Alignment of PDB Files

Read AMBER Binary netCDF files

Add a Sequence to an Existing Alignmnet

View CNA Protein Structure Network Community Output in VMD

Percent Identity Filter

Vector Field Visualization of Modes

Run Length Encoding with Indices

Radius of Gyration

Visualization of Dynamic Cross-Correlation

Write PIR Formated Sequences

network.amendment

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

Store all-atom data from a PDB object

Read PQR output from pdcBD File

Plot a Summary of HMMER Hit Statistics.

Atom Selection From PDB Structure

NCBI BLAST Sequence Search

Principal Component Analysis

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

Printing Core Positions and Returning Indices

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

Download FASTA Sequence Files

HMMER Sequence Search

NMA Atomic Displacement Trajectory

GeoStaS Domain Finder

Calculate the Angle Between Three Atoms

AAindex: Amino Acid Index Database

Amino Acid Residue Mass

Dendrogram with Clustering Annotation

Prune A cna Network Object

Create a HTML Page For a Given Alignment

SSE Backbone Hydrogen Bonding

Protein Structure Network Layout

VMD Color Palette

Summarize and Print Features of a cna Network Graph

Sequence Consensus for an Alignment

Is an Object of Class xyz?

Calculate the Distances Between the Rows of Two Matrices

PCA / NMA Atomic Displacement Trajectory

Find Sequence Motifs.

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Plot Core Fitting Progress

Square Inner Product

Root Mean Square Deviation

Trim a PDB Object To A Subset of Atoms.

Fetch UniProt Entry Data.

Wrap Torsion Angle Data

Orient a PDB Structure

Combine Atom Selections From PDB Structure

PDBs to PDB Converter

Is an Object of Class select?

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Printing Sequence Alignments