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bio3d (version 2.1-3)

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.

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Version

Install

install.packages('bio3d')

Monthly Downloads

2,809

Version

2.1-3

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Barry Grant

Last Published

October 27th, 2014

Functions in bio3d (2.1-3)

Contact Map Consensus Filtering

Atom Names/Types

Bio3d Example Data

Secondary Structure Analysis of Trajectories with DSSP

Mass-weighted Inner Product

deformation.nma

Deformation Analysis

PCA Atomic Displacement Trajectory

Convert Between 1-letter and 3-letter Aminoacid Codes

Identify Points in a CNA Protein Structure Network Plot

Convert an Aminoacid Sequence to AAIndex Values

Principal Component Analysis

NCBI BLAST Sequence Search

network.amendment

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

Atom Names/Types to Atomic Symbols Converter

Filter for Cross-correlation Matrices (Cij)

Calculate the Distances Between the Rows of Two Matrices

HMMER Sequence Search

Convert Between Atom and xyz Indices

Chemical Formula to Mass Converter

Renumber and Convert Between Various PDB formats

Principal Component Analysis

Amino Acid Residues to Mass Converter

Percent Identity Filter

Plot NMA Results

normalize.vector

Mass-Weighted Normalized Vector

Binding Site Residues

difference.vector

Difference Vector

Root Mean Square Deviation

Diagonal Indices of a Matrix

Dynamic Cross-Correlation from Principal Component Analysis

Calculate Covariance Matrix from Normal Modes

DCCM: Dynamical Cross-Correlation Matrix

LMI: Linear Mutual Information Matrix

AAindex: Amino Acid Index Database

PDBs to PDB Converter

Read FASTA formated Sequences

Score Residue Conservation At Each Position in an Alignment

Bhattacharyya Coefficient

PDB File Coordinate Superposition

Amino Acid Residue Mass

Biological Structure Analysis

Ensemble Normal Mode Analysis

Calculate the Angle Between Three Atoms

Read Aligned Structure Data

Distance Matrix Analysis

Atom Names/Types to Mass Converter

Cross-Correlation for Ensemble NMA (eNMA)

Is an Object of Class xyz?

Covariance Overlap

Read PQR output from pdcBD File

Download FASTA Sequence Files

Is an Object of Class select?

Periodic Table of the Elements

Read AMBER Binary netCDF files

Sequence Alignment of PDB Files

PCA / NMA Atomic Displacement Trajectory

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Find Possible PDB Chain Breaks

NMA Fluctuations

Check on Missing Utility Programs

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

VMD Color Palette

Get Customizable Annotations From PDB

Plot Distance Matrix

Combine Sequences by Rows Without Recycling

Coordinate Superposition

Add a Sequence to an Existing Alignmnet

Filter or Trim a pdbs PDBs Object

Principal Component Analysis

Create a HTML Page For a Given Alignment

Bounds of a Numeric Vector

Principal Component Analysis of an arrary of matrices

Atomic RMS Fluctuations

Setup for Running Bio3D Functions using Multiple CPU Cores

Plot a Summary of HMMER Hit Statistics.

Extract The Aminoacid Sequence From A PDB Object

Dynamic Cross-Correlation from Normal Modes Analysis

Secondary Structure Analysis of Aligned PDB Structures with DSSP

Identification of Invariant Core Positions

Write FASTA Formated Sequences

Shannon Entropy Score

Normal Mode Analysis

Download PDB Coordinate Files

Project Data onto Principal Components

Protein Structure Network Plots in 2D and 3D.

Plot eNMA Results

inspect.connectivity

Check the Connectivity of Protein Structures

Combine Atom Selections From PDB Structure

GeoStaS Domain Finder

Is an Object of Class pdb(s)?

ENM Force Field Loader

DCCM: Dynamical Cross-Correlation Matrix

Normal Mode Analysis

Dendrogram with Clustering Annotation

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

NMA Atomic Displacement Trajectory

Plot PCA Results

Plot Core Fitting Progress

Overlap analysis

Write PIR Formated Sequences

Plot a Summary of BLAST Hit Statistics.

Square Inner Product

Printing XYZ coordinates

Visualization of Dynamic Cross-Correlation

Read Aligned Structure Data

Pairwise Distance Variance in Cartesian Coordinates

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Mapping between PDB atomic indices and alignment positions

Plot a Multiple Sequence Alignment

Printing Sequence Alignments

Read CHARMM/X-PLOR/NAMD Binary DCD files

Structure Alignment Of Two PDB Files

Plot RMSIP Results

Calculate Torsion/Dihedral Angles

Protein Structure Network Layout

Replicate Per-residue Vector Values

Store all-atom data from a PDB object

Printing Core Positions and Returning Indices

View CNA Protein Structure Network Community Output in VMD

Prune A cna Network Object

Trim a PDB Object To A Subset of Atoms.

Vector Field Visualization of Modes

Sequence Alignment of Identical Protein Sequences

Radius of Gyration

Write PDB Format Coordinate File

Wrap Torsion Angle Data

Root Mean Square Inner Product

Alignment Gap Summary

Orient a PDB Structure

Run Length Encoding with Indices

Percent Identity

SSE Backbone Hydrogen Bonding

Fetch UniProt Entry Data.

Plots with marginal SSE annotation

Write PQR Format Coordinate File

Atom Selection From PDB Structure

Secondary Structure Analysis with DSSP or STRIDE

Download Pfam FASTA Sequence Alignment

Summarize and Print Features of a cna Network Graph

Principal Component Analysis

Protein Dynamic Correlation Network Construction and Community Analysis.

Sequence Consensus for an Alignment

Find Sequence Motifs.

Structure-based Sequence Alignment with MUSTANG

List all Functions in the bio3d Package

Sequence Alignment with MUSCLE

Align a PDB structure to an existing alignment

Ensemble NMA Atomic Displacement Trajectory

Index for the sdENM ff

Sequence Generation from a Bounds Vector

Write AMBER Binary netCDF files