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bio3d (version 2.1-2)

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

2.1-2

License

GPL (>= 2)

Homepage

http://thegrantlab.org/bio3d/

Maintainer

Barry Grant

Last Published

October 21st, 2014

Functions in bio3d (2.1-2)

Check on Missing Utility Programs

Contact Map Consensus Filtering

Combine Atom Selections From PDB Structure

LMI: Linear Mutual Information Matrix

Convert Between 1-letter and 3-letter Aminoacid Codes

NMA Fluctuations

Dynamic Cross-Correlation from Principal Component Analysis

Is an Object of Class select?

Amino Acid Residue Mass

Atom Names/Types

Is an Object of Class pdb(s)?

NCBI BLAST Sequence Search

Dynamic Cross-Correlation from Normal Modes Analysis

Bounds of a Numeric Vector

Alignment Gap Summary

Convert an Aminoacid Sequence to AAIndex Values

Calculate the Angle Between Three Atoms

Biological Structure Analysis

Atom Names/Types to Mass Converter

Cross-Correlation for Ensemble NMA (eNMA)

Binding Site Residues

Mapping between PDB atomic indices and alignment positions

Printing Core Positions and Returning Indices

Atom Names/Types to Atomic Symbols Converter

DCCM: Dynamical Cross-Correlation Matrix

inspect.connectivity

Check the Connectivity of Protein Structures

Principal Component Analysis

Periodic Table of the Elements

Covariance Overlap

AAindex: Amino Acid Index Database

DCCM: Dynamical Cross-Correlation Matrix

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

Plot RMSIP Results

Identification of Invariant Core Positions

Shannon Entropy Score

Principal Component Analysis

Sequence Alignment of PDB Files

Find Possible PDB Chain Breaks

Protein Dynamic Correlation Network Construction and Community Analysis.

Plot NMA Results

Percent Identity

network.amendment

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

ENM Force Field Loader

Dendrogram with Clustering Annotation

Plots with marginal SSE annotation

Calculate Torsion/Dihedral Angles

Sequence Generation from a Bounds Vector

Overlap analysis

Protein Structure Network Layout

Atom Selection From PDB Structure

Setup for Running Bio3D Functions using Multiple CPU Cores

Convert Between Atom and xyz Indices

Mass-weighted Inner Product

Structure-based Sequence Alignment with MUSTANG

Orient a PDB Structure

Calculate the Distances Between the Rows of Two Matrices

Principal Component Analysis of an arrary of matrices

difference.vector

Difference Vector

Identify Points in a CNA Protein Structure Network Plot

Extract The Aminoacid Sequence From A PDB Object

Find Sequence Motifs.

Download FASTA Sequence Files

Renumber and Convert Between Various PDB formats

Diagonal Indices of a Matrix

Secondary Structure Analysis with DSSP or STRIDE

Write PIR Formated Sequences

Read Aligned Structure Data

Plot eNMA Results

Distance Matrix Analysis

List all Functions in the bio3d Package

Filter for Cross-correlation Matrices (Cij)

Normal Mode Analysis

Printing XYZ coordinates

Secondary Structure Analysis of Aligned PDB Structures with DSSP

Download PDB Coordinate Files

Protein Structure Network Plots in 2D and 3D.

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

Chemical Formula to Mass Converter

deformation.nma

Deformation Analysis

Is an Object of Class xyz?

normalize.vector

Mass-Weighted Normalized Vector

Download Pfam FASTA Sequence Alignment

Principal Component Analysis

Prune A cna Network Object

Bhattacharyya Coefficient

Coordinate Superposition

Score Residue Conservation At Each Position in an Alignment

Create a HTML Page For a Given Alignment

Plot Distance Matrix

Read FASTA formated Sequences

Sequence Alignment with MUSCLE

Plot a Summary of BLAST Hit Statistics.

Combine Sequences by Rows Without Recycling

NMA Atomic Displacement Trajectory

Normal Mode Analysis

Bio3d Example Data

Structure Alignment Of Two PDB Files

Get Customizable Annotations From PDB

Visualization of Dynamic Cross-Correlation

Write AMBER Binary netCDF files

Summarize and Print Features of a cna Network Graph

Project Data onto Principal Components

PCA Atomic Displacement Trajectory

Radius of Gyration

Atomic RMS Fluctuations

Index for the sdENM ff

Read AMBER Binary netCDF files

Filter or Trim a pdbs PDBs Object

Trim a PDB Object To A Subset of Atoms.

Square Inner Product

Plot a Summary of HMMER Hit Statistics.

Store all-atom data from a PDB object

Fetch UniProt Entry Data.

Sequence Alignment of Identical Protein Sequences

PDB File Coordinate Superposition

Run Length Encoding with Indices

Vector Field Visualization of Modes

Principal Component Analysis

PCA / NMA Atomic Displacement Trajectory

Add a Sequence to an Existing Alignmnet

Pairwise Distance Variance in Cartesian Coordinates

Printing Sequence Alignments

VMD Color Palette

Read CHARMM/X-PLOR/NAMD Binary DCD files

Root Mean Square Deviation

Align a PDB structure to an existing alignment

Plot Core Fitting Progress

PDBs to PDB Converter

plot.pca.loadings

Plot Residue Loadings along PC1 to PC3

Write PDB Format Coordinate File

Read Aligned Structure Data

Plot PCA Results

SSE Backbone Hydrogen Bonding

Replicate Per-residue Vector Values

Write FASTA Formated Sequences

View CNA Protein Structure Network Community Output in VMD

Write PQR Format Coordinate File

Calculate Covariance Matrix from Normal Modes

GeoStaS Domain Finder

Secondary Structure Analysis of Trajectories with DSSP

Sequence Consensus for an Alignment

HMMER Sequence Search

Plot a Multiple Sequence Alignment

Percent Identity Filter

Ensemble NMA Atomic Displacement Trajectory

Ensemble Normal Mode Analysis

Read PQR output from pdcBD File

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Amino Acid Residues to Mass Converter

Root Mean Square Inner Product

Wrap Torsion Angle Data