| Biological Structure Analysis | bio3d-package bio3d |
| AAindex: Amino Acid Index Database | aa.index |
| Table of Relevant Amino Acids | aa.table |
| Convert Between 1-letter and 3-letter Aminoacid Codes | aa123 aa321 |
| Convert an Aminoacid Sequence to AAIndex Values | aa2index |
| Amino Acid Residues to Mass Converter | aa2mass |
| All Atom Normal Mode Analysis | aanma aanma.pdb rtb |
| Ensemble Normal Mode Analysis with All-Atom ENM | aanma.pdbs |
| Create a HTML Page For a Given Alignment | aln2html |
| Calculate the Angle Between Three Atoms | angle.xyz |
| Alignment to FASTA object | as.fasta |
| Convert to PDB format | as.pdb as.pdb.default as.pdb.mol2 as.pdb.prmtop |
| Convert Atomic Indices to a Select Object | as.select |
| Atom Names/Types | atom.index |
| Atom Selection from PDB and PRMTOP Structure Objects | atom.select atom.select.mol2 atom.select.pdb atom.select.pdbs atom.select.prmtop print.select |
| Atom Names/Types to Atomic Symbols Converter | atom2ele atom2ele.default atom2ele.pdb |
| Atom Names/Types to Mass Converter | atom2mass atom2mass.default atom2mass.pdb |
| Convert Between Atom and xyz Indices | atom2xyz xyz2atom |
| Manipulate PDB File Names | basename.pdb |
| Bhattacharyya Coefficient | bhattacharyya bhattacharyya.array bhattacharyya.enma bhattacharyya.matrix bhattacharyya.nma bhattacharyya.pca |
| Binding Site Residues | binding.site |
| Biological Units Construction | biounit |
| NCBI BLAST Sequence Search and Summary Plot of Hit Statistics | blast.pdb get.blast plot.blast |
| Bounds of a Numeric Vector | bounds |
| Obtain A SSE Object From An SSE Sequence Vector | bounds.sse |
| Color Palettes | bwr.colors mono.colors |
| Concatenate Multiple PDB Objects | cat.pdb |
| Find Possible PDB Chain Breaks | chain.pdb |
| Check on Missing Utility Programs | check.utility |
| Inspect And Clean Up A PDB Object | clean.pdb |
| Contact Map | cmap cmap.default cmap.pdb cmap.pdbs cmap.xyz |
| Protein Dynamic Correlation Network Construction and Community Analysis. | cna cna.dccm cna.ensmb |
| Suboptimal Path Analysis for Correlation Networks | cnapath plot.cnapath plot.ecnapath print.cnapath summary.cnapath |
| Center of Mass | com com.pdb com.xyz |
| Combine Atom Selections From PDB Structure | combine.select |
| Align communities from two or more networks | community.aln |
| Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object. | community.tree |
| Sequence Consensus for an Alignment | consensus |
| Score Residue Conservation At Each Position in an Alignment | conserv |
| Renumber and Convert Between Various PDB formats | convert.pdb |
| Identification of Contact Map Core Positions | core.cmap |
| Identification of Invariant Core Positions | core.find core.find.default core.find.pdb core.find.pdbs |
| Calculate Covariance Matrix from Normal Modes | cov.enma cov.nma |
| Covariance Overlap | covsoverlap covsoverlap.enma covsoverlap.nma |
| DCCM: Dynamical Cross-Correlation Matrix | dccm |
| Cross-Correlation for Ensemble NMA (eNMA) | dccm.enma |
| Dynamic Cross-Correlation from Gaussian Network Model | dccm.egnm dccm.gnm |
| Dynamic Cross-Correlation from Normal Modes Analysis | dccm.nma |
| Dynamical Cross-Correlation Matrix from Principal Component Analysis | dccm.pca |
| Dynamical Cross-Correlation Matrix from Cartesian Coordinates | dccm.xyz |
| Deformation Analysis | deformation.nma |
| Diagonal Indices of a Matrix | diag.ind |
| Difference Vector | difference.vector |
| Calculate the Distances Between the Rows of Two Matrices | dist.xyz |
| Distance Matrix Analysis | dm dm.pdb dm.pdbs dm.xyz |
| Secondary Structure Analysis with DSSP or STRIDE | dssp dssp.pdb dssp.pdbs dssp.xyz print.sse stride |
| Periodic Table of the Elements | elements |
| Shannon Entropy Score | entropy |
| Bio3d Example Data | annotation core example.data hivp kinesin pdbs transducin |
| Contact Map Consensus Filtering | filter.cmap |
| Filter for Cross-correlation Matrices (Cij) | filter.dccm |
| Percent Identity Filter | filter.identity |
| RMSD Filter | filter.rmsd |
| Coordinate Superposition | fit.xyz rot.lsq |
| NMA Fluctuations | fluct.nma |
| Chemical Formula to Mass Converter | formula2mass |
| Alignment Gap Summary | gap.inspect |
| GeoStaS Domain Finder | amsm.xyz geostas geostas.default geostas.enma geostas.nma geostas.pdb geostas.pdbs geostas.xyz print.geostas |
| Download PDB Coordinate Files | get.pdb |
| Download FASTA Sequence Files | get.seq |
| Gaussian Network Model | gnm gnm.pdb gnm.pdbs |
| Dendrogram with Clustering Annotation | hclustplot |
| HMMER Sequence Search | hmmer |
| Identify Points in a CNA Protein Structure Network Plot | identify.cna |
| Mass-weighted Inner Product | inner.prod |
| Check the Connectivity of Protein Structures | inspect.connectivity |
| Gap Characters | is.gap |
| Is an Object of Class 'mol2'? | is.mol2 |
| Is an Object of Class 'pdb(s)'? | is.pdb is.pdbs |
| Is an Object of Class 'select'? | is.select |
| Is an Object of Class 'xyz'? | as.xyz is.xyz |
| Protein Structure Network Layout | layout.cna |
| List all Functions in the bio3d Package | lbio3d |
| ENM Force Field Loader | ff.aaenm ff.aaenm2 ff.anm ff.calpha ff.pfanm ff.reach ff.sdenm load.enmff |
| Mask a Subset of Atoms in a DCCM Object. | mask mask.dccm |
| PCA / NMA Atomic Displacement Trajectory | mktrj mktrj.enma mktrj.nma mktrj.pca |
| Find Sequence Motifs. | motif.find |
| Structure-based Sequence Alignment with MUSTANG | mustang |
| Amendment of a CNA Network According To A Input Community Membership Vector. | network.amendment |
| Normal Mode Analysis | nma |
| Normal Mode Analysis | build.hessian nma.pdb print.nma |
| Ensemble Normal Mode Analysis | nma.pdbs print.enma |
| Mass-Weighted Normalized Vector | normalize.vector |
| Orient a PDB Structure | orient.pdb |
| Overlap analysis | overlap |
| Pair Indices | pairwise |
| Principal Component Analysis | pca |
| Principal Component Analysis of an array of matrices | pca.array |
| Principal Component Analysis | pca.pdbs |
| Principal Component Analysis | pca.tor |
| Principal Component Analysis | pca.xyz print.pca |
| Get Customizable Annotations From PDB Or PFAM Databases | pdb.annotate pdb.pfam |
| Align a PDB structure to an existing alignment | pdb2aln |
| Mapping from alignment positions to PDB atomic indices | pdb2aln.ind |
| Obtain An SSE Sequence Vector From A PDB Object | pdb2sse |
| Sequence Alignment of PDB Files | pdbaln |
| PDB File Coordinate Superposition | pdbfit pdbfit.pdb pdbfit.pdbs |
| PDBs to PDB Converter | pdbs2pdb |
| SSE annotation for a PDBs Object | pdbs2sse |
| Extract The Aminoacid Sequence From A PDB Object | pdbseq |
| Split a PDB File Into Separate Files, One For Each Chain. | pdbsplit |
| Download Pfam FASTA Sequence Alignment | pfam |
| Plots with marginal SSE annotation | plot.bio3d plotb3 |
| Plot Contact Matrix | plot.cmap |
| Protein Structure Network Plots in 2D and 3D. | plot.cna plot.ecna |
| Plot Core Fitting Progress | plot.core |
| DCCM Plot | plot.dccm |
| Plot Distance Matrix | plot.dmat |
| Plot eNMA Results | plot.enma |
| Plot a Multiple Sequence Alignment | plot.fasta |
| Plot Fluctuations | plot.fluct |
| Plot Geostas Results | plot.geostas |
| Plot a Summary of HMMER Hit Statistics. | plot.hmmer |
| Plot Residue-Residue Matrix Loadings | plot.matrix.loadings |
| Plot NMA Results | plot.nma |
| Plot PCA Results | plot.pca plot.pca.score plot.pca.scree |
| Plot Residue Loadings along PC1 to PC3 | plot.pca.loadings |
| Plot RMSIP Results | plot.rmsip |
| Summarize and Print Features of a cna Network Graph | print.cna summary.cna |
| Printing Core Positions and Returning Indices | print.core |
| Printing Sequence Alignments | .print.fasta.ali print.fasta |
| Printing XYZ coordinates | print.xyz |
| Project Data onto Principal Components | project.pca xyz2z.pca z2xyz.pca |
| Prune A cna Network Object | prune.cna |
| Biomolecular Visualization with PyMOL | pymol pymol.dccm pymol.modes pymol.nma pymol.pca pymol.pdbs |
| Read Aligned Structure Data | read.all |
| Read mmCIF File | read.cif |
| Read Coordinate Data from Amber or Charmm | read.crd |
| Read AMBER Coordinate files | read.crd.amber |
| Read CRD File | read.crd.charmm |
| Read CHARMM/X-PLOR/NAMD Binary DCD files | read.dcd |
| Read FASTA formated Sequences | read.fasta |
| Read Aligned Structure Data | read.fasta.pdb |
| Read MOL2 File | print.mol2 read.mol2 |
| Read AMBER Binary netCDF files | read.ncdf |
| Read PDB File | print.pdb read.pdb read.pdb2 summary.pdb |
| Read PQR output from pdcBD File | read.pdcBD |
| Read PQR File | read.pqr |
| Read AMBER Parameter/Topology files | print.prmtop read.prmtop |
| Radius of Gyration | rgyr |
| Run Length Encoding with Indices | print.rle2 rle2 |
| Root Mean Square Deviation | rmsd |
| Atomic RMS Fluctuations | rmsf |
| Root Mean Square Inner Product | rmsip rmsip.default rmsip.enma |
| Index for the sdENM ff | sdENM |
| Add a Sequence to an Existing Alignmnet | seq2aln |
| Sequence Alignment with MUSCLE | seqaln |
| Sequence Alignment of Identical Protein Sequences | seqaln.pair |
| Combine Sequences by Rows Without Recycling | seqbind |
| Percent Identity | seqidentity |
| Setup for Running Bio3D Functions using Multiple CPU Cores | setup.ncore |
| Square Inner Product | sip sip.default sip.enma sip.nma |
| SSE Backbone Hydrogen Bonding | sse.bridges |
| Store all-atom data from a PDB object | store.atom |
| Structure Alignment Of Two PDB Files | struct.aln |
| Calculate Mainchain and Sidechain Torsion/Dihedral Angles | torsion.pdb |
| Calculate Torsion/Dihedral Angles | torsion.xyz |
| Trim a PDB Object To A Subset of Atoms. | trim trim.pdb |
| Trim a MOL2 Object To A Subset of Atoms. | trim.mol2 |
| Filter or Trim a PDBs Object | trim.pdbs |
| Trim a XYZ Object of Cartesian Coordinates. | trim.xyz |
| Sequence Generation from a Bounds Vector | unbound |
| Fetch UniProt Entry Data. | uniprot |
| Pairwise Distance Variance in Cartesian Coordinates | var.pdbs var.xyz |
| Replicate Per-residue Vector Values | vec2resno |
| View CNA Protein Structure Network Community Output in VMD | vmd vmd.cna vmd.cnapath vmd.ecna vmd.ecnapath |
| VMD Color Palette | vmd_colors |
| Wrap Torsion Angle Data | wrap.tor |
| Write CRD File | write.crd |
| Write FASTA Formated Sequences | write.fasta |
| Write MOL2 Format Coordinate File | write.mol2 |
| Write AMBER Binary netCDF files | write.ncdf |
| Write PDB Format Coordinate File | write.pdb |
| Write PIR Formated Sequences | write.pir |
| Write PQR Format Coordinate File | write.pqr |
