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
Color Palettes
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
Contact Map
Protein Dynamic Correlation Network Construction and Community Analysis.
Coordinate Superposition
Contact Map Consensus Filtering
RMSD Filter
Normal Mode Analysis
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
Mass-weighted Inner Product
GeoStaS Domain Finder
Calculate the Distances Between the Rows of Two Matrices
Ensemble Normal Mode Analysis
Mass-Weighted Normalized Vector
Orient a PDB Structure
Check the Connectivity of Protein Structures
Plot Distance Matrix
Is an Object of Class ‘pdb(s)’?
List all Functions in the bio3d Package
DCCM Plot
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 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
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
Pair Indices
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
Center of Mass
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
Read PQR File
Atomic RMS Fluctuations
Store all-atom data from a PDB object
Combine Sequences by Rows Without Recycling
Root Mean Square Inner Product
Read CRD File
Read Aligned Structure Data
Percent Identity
Protein Structure Network Layout
Gap Characters
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
Read MOL2 File
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 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
Read PDB File
Pairwise Distance Variance in Cartesian Coordinates
Fetch UniProt Entry Data.
Write PDB Format Coordinate File
Write CRD File
Write PIR Formated Sequences
Write FASTA Formated Sequences