bio3d

AAindex: Amino Acid Index Database

Table of Relevant Amino Acids

Convert Between 1-letter and 3-letter Aminoacid Codes

Convert an Aminoacid Sequence to AAIndex Values

Amino Acid Residues to Mass Converter

All Atom Normal Mode Analysis

Ensemble Normal Mode Analysis with All-Atom ENM

Create a HTML Page For a Given Alignment

Calculate the Angle Between Three Atoms

Alignment to FASTA object

Convert to PDB format

Convert Atomic Indices to a Select Object

Atom Names/Types

Atom Selection from PDB and PRMTOP Structure Objects

Atom Names/Types to Atomic Symbols Converter

Atom Names/Types to Mass Converter

Convert Between Atom and xyz Indices

Manipulate PDB File Names

Bhattacharyya Coefficient

Binding Site Residues

Biological Structure Analysis

Biological Units Construction

NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

Bounds of a Numeric Vector

Obtain A SSE Object From An SSE Sequence Vector

Color Palettes

Concatenate Multiple PDB Objects

Find Possible PDB Chain Breaks

Check on Missing Utility Programs

Inspect And Clean Up A PDB Object

Contact Map

Protein Dynamic Correlation Network Construction and Community Analysis.

Suboptimal Path Analysis for Correlation Networks

Center of Mass

Combine Atom Selections From PDB Structure

Align communities from two or more networks

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

Sequence Consensus for an Alignment

Score Residue Conservation At Each Position in an Alignment

Renumber and Convert Between Various PDB formats

Identification of Contact Map Core Positions

Identification of Invariant Core Positions

Calculate Covariance Matrix from Normal Modes

Covariance Overlap

DCCM: Dynamical Cross-Correlation Matrix

Cross-Correlation for Ensemble NMA (eNMA)

Dynamic Cross-Correlation from Gaussian Network Model

Dynamic Cross-Correlation from Normal Modes Analysis

Dynamical Cross-Correlation Matrix from Principal Component Analysis

Dynamical Cross-Correlation Matrix from Cartesian Coordinates

Deformation Analysis

Diagonal Indices of a Matrix

Difference Vector

Calculate the Distances Between the Rows of Two Matrices

Distance Matrix Analysis

Secondary Structure Analysis with DSSP or STRIDE

Periodic Table of the Elements

Shannon Entropy Score

Bio3d Example Data

Contact Map Consensus Filtering

Filter for Cross-correlation Matrices (Cij)

Percent Identity Filter

RMSD Filter

Coordinate Superposition

NMA Fluctuations

Chemical Formula to Mass Converter

Alignment Gap Summary

GeoStaS Domain Finder

Download PDB Coordinate Files

Download FASTA Sequence Files

Gaussian Network Model

Dendrogram with Clustering Annotation

HMMER Sequence Search

Identify Points in a CNA Protein Structure Network Plot

Mass-weighted Inner Product

Check the Connectivity of Protein Structures

Gap Characters

Is an Object of Class ‘mol2’?

Is an Object of Class ‘pdb(s)’?

Is an Object of Class ‘select’?

Is an Object of Class ‘xyz’?

Protein Structure Network Layout

List all Functions in the bio3d Package

ENM Force Field Loader

Mask a Subset of Atoms in a DCCM Object.

PCA / NMA Atomic Displacement Trajectory

Find Sequence Motifs.

Structure-based Sequence Alignment with MUSTANG

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

Normal Mode Analysis

Normal Mode Analysis

Ensemble Normal Mode Analysis

Mass-Weighted Normalized Vector

Orient a PDB Structure

Overlap analysis

Pair Indices

Principal Component Analysis

Principal Component Analysis of an array of matrices

Principal Component Analysis

Principal Component Analysis

Principal Component Analysis

Get Customizable Annotations From PDB Or PFAM Databases

Align a PDB structure to an existing alignment

Mapping from alignment positions to PDB atomic indices

Obtain An SSE Sequence Vector From A PDB Object

Sequence Alignment of PDB Files

PDB File Coordinate Superposition

PDBs to PDB Converter

SSE annotation for a PDBs Object

Extract The Aminoacid Sequence From A PDB Object

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

Download Pfam FASTA Sequence Alignment

Plots with marginal SSE annotation

Plot Contact Matrix

Protein Structure Network Plots in 2D and 3D.

Plot Core Fitting Progress

DCCM Plot

Plot Distance Matrix

Plot eNMA Results

Plot a Multiple Sequence Alignment

Plot Fluctuations

Plot Geostas Results

Plot a Summary of HMMER Hit Statistics.

Plot Residue-Residue Matrix Loadings

Plot NMA Results

Plot PCA Results

Plot Residue Loadings along PC1 to PC3

Plot RMSIP Results

Summarize and Print Features of a cna Network Graph

Printing Core Positions and Returning Indices

Printing Sequence Alignments

Printing XYZ coordinates

Project Data onto Principal Components

Prune A cna Network Object

Biomolecular Visualization with PyMOL

Read Aligned Structure Data

Read mmCIF File

Read Coordinate Data from Amber or Charmm

Read AMBER Coordinate files

Read CRD File

Read CHARMM/X-PLOR/NAMD Binary DCD files

Read FASTA formated Sequences

Read Aligned Structure Data

Read MOL2 File

Read AMBER Binary netCDF files

Read PDB File

Read PQR output from pdcBD File

Read PQR File

Read AMBER Parameter/Topology files

Radius of Gyration

Run Length Encoding with Indices

Root Mean Square Deviation

Atomic RMS Fluctuations

Root Mean Square Inner Product

Index for the sdENM ff

Add a Sequence to an Existing Alignmnet

Sequence Alignment with MUSCLE

Sequence Alignment of Identical Protein Sequences

Combine Sequences by Rows Without Recycling

Percent Identity

Setup for Running Bio3D Functions using Multiple CPU Cores

Square Inner Product

SSE Backbone Hydrogen Bonding

Store all-atom data from a PDB object

Structure Alignment Of Two PDB Files

Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Calculate Torsion/Dihedral Angles

Trim a MOL2 Object To A Subset of Atoms.

Trim a PDB Object To A Subset of Atoms.

Filter or Trim a PDBs Object

Trim a XYZ Object of Cartesian Coordinates.

Sequence Generation from a Bounds Vector

Fetch UniProt Entry Data.

Pairwise Distance Variance in Cartesian Coordinates

Replicate Per-residue Vector Values

View CNA Protein Structure Network Community Output in VMD

VMD Color Palette

Wrap Torsion Angle Data

Write CRD File

Write FASTA Formated Sequences

Write MOL2 Format Coordinate File

Write AMBER Binary netCDF files

Write PDB Format Coordinate File

Write PIR Formated Sequences

Write PQR Format Coordinate File