Amino Acid Residues to Mass Converter
All Atom Normal Mode Analysis
Ensemble Normal Mode Analysis with All-Atom ENM
Convert Between 1-letter and 3-letter Aminoacid Codes
Calculate the Angle Between Three Atoms
Table of Relevant Amino Acids
Convert an Aminoacid Sequence to AAIndex Values
AAindex: Amino Acid Index Database
Create a HTML Page For a Given Alignment
Alignment to FASTA object
Atom Names/Types to Atomic Symbols Converter
Manipulate PDB File Names
Atom Selection from PDB and PRMTOP Structure Objects
Bhattacharyya Coefficient
Binding Site Residues
Atom Names/Types
Convert Atomic Indices to a Select Object
Convert Between Atom and xyz Indices
Atom Names/Types to Mass Converter
Convert to PDB format
Biological Structure Analysis
Obtain A SSE Object From An SSE Sequence Vector
Concatenate Multiple PDB Objects
Color Palettes
Inspect And Clean Up A PDB Object
NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
Check on Missing Utility Programs
Find Possible PDB Chain Breaks
Bounds of a Numeric Vector
Biological Units Construction
Protein Dynamic Correlation Network Construction and Community Analysis.
Suboptimal Path Analysis for Correlation Networks
Score Residue Conservation At Each Position in an Alignment
Align communities from two or more networks
Center of Mass
Contact Map
Combine Atom Selections From PDB Structure
Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object.
Renumber and Convert Between Various PDB formats
Sequence Consensus for an Alignment
Cross-Correlation for Ensemble NMA (eNMA)
Covariance Overlap
Dynamic Cross-Correlation from Normal Modes Analysis
DCCM: Dynamical Cross-Correlation Matrix
Identification of Contact Map Core Positions
Calculate Covariance Matrix from Normal Modes
Dynamical Cross-Correlation Matrix from Cartesian Coordinates
Identification of Invariant Core Positions
Dynamic Cross-Correlation from Gaussian Network Model
Periodic Table of the Elements
Diagonal Indices of a Matrix
Deformation Analysis
Dynamical Cross-Correlation Matrix from Principal Component Analysis
Shannon Entropy Score
Difference Vector
Calculate the Distances Between the Rows of Two Matrices
Contact Map Consensus Filtering
Distance Matrix Analysis
Bio3d Example Data
Download FASTA Sequence Files
Download PDB Coordinate Files
Alignment Gap Summary
GeoStaS Domain Finder
Filter for Cross-correlation Matrices (Cij)
Coordinate Superposition
Percent Identity Filter
RMSD Filter
Secondary Structure Analysis with DSSP or STRIDE
NMA Fluctuations
Is an Object of Class ‘select’?
Identify Points in a CNA Protein Structure Network Plot
Chemical Formula to Mass Converter
Is an Object of Class ‘pdb(s)’?
HMMER Sequence Search
Gaussian Network Model
Dendrogram with Clustering Annotation
Amendment of a CNA Network According To A Input Community Membership Vector.
Structure-based Sequence Alignment with MUSTANG
Gap Characters
Is an Object of Class ‘mol2’?
Find Sequence Motifs.
Check the Connectivity of Protein Structures
Is an Object of Class ‘xyz’?
Mass-weighted Inner Product
Protein Structure Network Layout
Mask a Subset of Atoms in a DCCM Object.
Principal Component Analysis
Normal Mode Analysis
Ensemble Normal Mode Analysis
Normal Mode Analysis
Principal Component Analysis
Orient a PDB Structure
PCA / NMA Atomic Displacement Trajectory
Mass-Weighted Normalized Vector
Extract The Aminoacid Sequence From A PDB Object
Pair Indices
Overlap analysis
Obtain An SSE Sequence Vector From A PDB Object
Principal Component Analysis of an array of matrices
SSE annotation for a PDBs Object
List all Functions in the bio3d Package
ENM Force Field Loader
Sequence Alignment of PDB Files
Principal Component Analysis
Get Customizable Annotations From PDB Or PFAM Databases
Principal Component Analysis
PDBs to PDB Converter
PDB File Coordinate Superposition
Plot a Multiple Sequence Alignment
Plot eNMA Results
Align a PDB structure to an existing alignment
Protein Structure Network Plots in 2D and 3D.
Plots with marginal SSE annotation
Mapping from alignment positions to PDB atomic indices
Plot Core Fitting Progress
Plot Distance Matrix
DCCM Plot
Plot Contact Matrix
Download Pfam FASTA Sequence Alignment
Split a PDB File Into Separate Files, One For Each Chain.
Plot Fluctuations
Plot a Summary of HMMER Hit Statistics.
Printing Core Positions and Returning Indices
Plot Residue Loadings along PC1 to PC3
Plot NMA Results
Plot Residue-Residue Matrix Loadings
Summarize and Print Features of a cna Network Graph
Plot RMSIP Results
Plot PCA Results
Plot Geostas Results
Read mmCIF File
Read CRD File
Read AMBER Coordinate files
Read Coordinate Data from Amber or Charmm
Prune A cna Network Object
Biomolecular Visualization with PyMOL
Project Data onto Principal Components
Printing Sequence Alignments
Read FASTA formated Sequences
Read Aligned Structure Data
Read Aligned Structure Data
Printing XYZ coordinates
Radius of Gyration
Read AMBER Parameter/Topology files
Read PDB File
Read AMBER Binary netCDF files
Read CHARMM/X-PLOR/NAMD Binary DCD files
Read PQR output from pdcBD File
Read PQR File
Read MOL2 File
Index for the sdENM ff
Add a Sequence to an Existing Alignmnet
Combine Sequences by Rows Without Recycling
Percent Identity
Atomic RMS Fluctuations
Root Mean Square Inner Product
Root Mean Square Deviation
Run Length Encoding with Indices
Setup for Running Bio3D Functions using Multiple CPU Cores
Trim a PDB Object To A Subset of Atoms.
Filter or Trim a PDBs Object
Square Inner Product
Calculate Torsion/Dihedral Angles
Store all-atom data from a PDB object
Trim a MOL2 Object To A Subset of Atoms.
Replicate Per-residue Vector Values
Sequence Alignment of Identical Protein Sequences
Sequence Alignment with MUSCLE
Pairwise Distance Variance in Cartesian Coordinates
Sequence Generation from a Bounds Vector
Fetch UniProt Entry Data.
SSE Backbone Hydrogen Bonding
Trim a XYZ Object of Cartesian Coordinates.
View CNA Protein Structure Network Community Output in VMD
Write PDB Format Coordinate File
Write AMBER Binary netCDF files
Write MOL2 Format Coordinate File
Write CRD File
Calculate Mainchain and Sidechain Torsion/Dihedral Angles
Structure Alignment Of Two PDB Files
Write FASTA Formated Sequences
VMD Color Palette
Wrap Torsion Angle Data
Write PQR Format Coordinate File
Write PIR Formated Sequences