Biological Structure Analysis
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 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 Analysi...
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 Obj...
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
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
DCCM: Dynamical Cross-Correlation Matrix
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
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 V...
Normal Mode Analysis
Ensemble Normal Mode Analysis
Normal Mode Analysis
Mass-Weighted Normalized Vector
Orient a PDB Structure
Overlap analysis
Pair Indices
Principal Component Analysis of an array of matrices
Principal Component Analysis
Principal Component Analysis
Principal Component Analysis
Principal Component Analysis
Get Customizable Annotations From PDB Or PFAM Databases
Mapping from alignment positions to PDB atomic indices
Align a PDB structure to an existing alignment
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 Residue Loadings along PC1 to PC3
Plot PCA Results
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 AMBER Coordinate files
Read CRD File
Read Coordinate Data from Amber or Charmm
Read CHARMM/X-PLOR/NAMD Binary DCD files
Read Aligned Structure Data
Read FASTA formated Sequences
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
Add a Sequence to an Existing Alignmnet
Sequence Alignment of Identical Protein Sequences
Sequence Alignment with MUSCLE
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
VMD Color Palette
View CNA Protein Structure Network Community Output in VMD
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
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.