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bio3d
Biological Structure Analysis
View on CRAN: Click
here
Download and install bio3d package within the R console
Install from CRAN:
install.packages("bio3d")
Install from Github:
library("remotes")
install_github("cran/bio3d") Install by package version:
library("remotes")
install_version("bio3d", "2.4-5") Attach the package and use:
library("bio3d")
Maintained by
Barry Grant
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-10-15
Latest Update: 2024-10-29
Description:
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.
How to cite:
Barry Grant (2014). bio3d: Biological Structure Analysis. R package version 2.4-5, https://cran.r-project.org/web/packages/bio3d. Accessed 10 Mar. 2026.
Previous versions and publish date:
2.1-1 (2014-10-15 23:57), 2.1-2 (2014-10-21 18:12), 2.1-3 (2014-10-27 19:03), 2.2-1 (2015-02-27 07:18), 2.2-2 (2015-03-03 07:34), 2.2-3 (2015-09-04 21:49), 2.2-4 (2015-12-12 09:12), 2.3-0 (2016-09-30 23:15), 2.3-1 (2016-11-12 00:27), 2.3-2 (2017-06-15 01:30), 2.3-3 (2017-07-31 06:23), 2.3-4 (2018-04-03 09:42), 2.4-0 (2019-11-26 18:40), 2.4-1 (2020-01-21 08:50), 2.4-2 (2021-05-11 09:02), 2.4-3 (2022-03-10 23:30), 2.4-4 (2022-10-27 00:45)
Other packages that cited bio3d R package
View bio3d citation profile
Other R packages that bio3d depends,
imports, suggests or enhances
Complete documentation for bio3d
Functions, R codes and Examples using
the bio3d R package
Some associated functions: aa.index . aa.table . aa123 . aa2index . aa2mass . aanma.pdb . aanma.pdbs . aln2html . angle.xyz . as.fasta . as.pdb . as.select . atom.index . atom.select . atom2ele . atom2mass . atom2xyz . basename.pdb . bhattacharyya . binding.site . bio3d.package . biounit . blast.pdb . bounds . bounds.sse . bwr.colors . cat.pdb . chain.pdb . check.utility . clean.pdb . cmap . cna . cnapath . com . combine.select . community.aln . community.tree . consensus . conserv . convert.pdb . core.cmap . core.find . cov.nma . covsoverlap . dccm.enma . dccm.gnm . dccm.nma . dccm . dccm.pca . dccm.xyz . deformation.nma . diag.ind . difference.vector . dist.xyz . dm . dssp . elements . entropy . example.data . filter.cmap . filter.dccm . filter.identity . filter.rmsd . fit.xyz . fluct.nma . formula2mass . gap.inspect . geostas . get.pdb . get.seq . gnm . hclustplot . hmmer . identify.cna . inner.prod . inspect.connectivity . is.gap . is.mol2 . is.pdb . is.select . is.xyz . layout.cna . lbio3d . load.enmff . mask.dccm . mktrj . motif.find . mustang . network.amendment . nma . nma.pdb . nma.pdbs . normalize.vector . orient.pdb . overlap . pairwise . pca.array . pca . pca.pdbs . pca.tor . pca.xyz . pdb.annotate . pdb2aln.ind . pdb2aln . pdb2sse . pdbaln . pdbfit . pdbs2pdb . pdbs2sse . pdbseq . pdbsplit . pfam . plot.bio3d . plot.cmap . plot.cna . plot.core . plot.dccm . plot.dmat . plot.enma . plot.fasta . plot.fluct . plot.geostas . plot.hmmer . plot.matrix.loadings . plot.nma . plot.pca.loadings . plot.pca . plot.rmsip . print.cna . print.core . print.fasta . print.xyz . project.pca . prune.cna . pymol . read.all . read.cif . read.crd.amber . read.crd.charmm . read.crd . read.dcd . read.fasta . read.fasta.pdb . read.mol2 . read.ncdf . read.pdb . read.pdcBD . read.pqr . read.prmtop . rgyr . rle2 . rmsd . rmsf . rmsip . sdENM . seq2aln . seqaln . seqaln.pair . seqbind . seqidentity . setup.ncore . sip . sse.bridges . store.atom . struct.aln . torsion.pdb . torsion.xyz . trim.mol2 . trim.pdb . trim.pdbs . trim.xyz . unbound . uniprot . var.xyz . vec2resno . vmd.cna . vmd_colors . wrap.tor . write.crd . write.fasta . write.mol2 . write.ncdf . write.pdb . write.pir . write.pqr .
Some associated R codes: RcppExports.R . aa123.R . aa2index.R . aa2mass.R . aa321.R . aanma.R . aanma.pdb.R . aanma.pdbs.R . aln2html.R . amsm.xyz.R . angle.xyz.R . arg_filter.R . as.fasta.R . as.pdb.R . as.pdb.mol2.R . as.pdb.prmtop.R . as.select.R . as.xyz.R . atom.select.R . atom.select.mol2.R . atom.select.pdb.R . atom.select.pdbs.R . atom.select.prmtop.R . atom2ele.R . atom2mass.R . atom2xyz.R . basename.pdb.R . bhattacharyya.R . binding.site.R . biounit.R . blast.pdb.R . bounds.R . bounds.sse.R . build.hessian.R . bwr.colors.R . cat.pdb.R . chain.pdb.R . check.utility.R . clean.pdb.R . cmap.R . cmap.pdb.R . cna.R . cna.dccm.R . cna.ensmb.R . cnapath.R . com.R . com.pdb.R . com.xyz.R . combine.select.R . community.aln.R . community.tree.R . consensus.R . conserv.R . convert.pdb.R . core.cmap.R . core.find.R . cov.nma.R . covsoverlap.R . dccm.R . dccm.enma.R . dccm.gnm.R . dccm.nma.R . dccm.pca.R . dccm.xyz.R . deformation.nma.R . diag.ind.R . difference.vector.R . dist.xyz.R . dm.R . dm.xyz.R . dssp.R . dssp.pdb.R . dssp.pdbs.R . dssp.xyz.R . entropy.R . exefile.R . filter.cmap.R . filter.dccm.R . filter.identity.R . filter.rmsd.R . fit.xyz.R . fluct.nma.R . formula2mass.R . gap.inspect.R . geostas.R . get.blast.R . get.pdb.R . get.seq.R . gnm.R . gnm.pdbs.R . hclustplot.R . hmmer.R . identify.cna.R . inner.prod.R . inspect.connectivity.R . is.gap.R . is.mol2.R . is.pdb.R . is.select.R . is.xyz.R . layout.cna.R . lbio3d.R . load.enmff.R . mask.dccm.R . mktrj.R . mktrj.enma.R . mktrj.nma.R . mktrj.pca.R . mono.colors.R . motif.find.R . mustang.R . network.amendment.R . nma.R . nma.pdb.R . nma.pdbs.R . nma_funs.R . normalize.vector.R . orient.pdb.R . overlap.R . pairwise.R . pb.R . pca.R . pca.array.R . pca.pdbs.R . pca.tor.R . pca.xyz.R . pdb.annotate.R . pdb.pfam.R . pdb2aln.R . pdb2aln.ind.R . pdb2sse.R . pdbaln.R . pdbfit.R . pdbs2pdb.R . pdbs2sse.R . pdbseq.R . pdbsplit.R . pfam.R . plot.blast.R . plot.cmap.R . plot.cna.R . plot.core.R . plot.dccm.R . plot.dmat.R . plot.enma.R . plot.fasta.R . plot.fluct.R . plot.geostas.R . plot.hmmer.R . plot.matrix.loadings.R . plot.nma.R . plot.pca.R . plot.pca.loadings.R . plot.pca.score.R . plot.pca.scree.R . plot.rmsip.R . plotb3.R . print.cna.R . print.core.R . print.enma.R . print.fasta.R . print.geostas.R . print.nma.R . print.pca.R . print.pdb.R . print.prmtop.R . print.select.R . print.sse.R . print.xyz.R . project.pca.R . prune.cna.R . pymol.dccm.R . pymol.modes.R . pymol.pdbs.R . read.all.R . read.cif.R . read.crd.R . read.crd.amber.R . read.crd.charmm.R . read.dcd.R . read.fasta.R . read.fasta.pdb.R . read.mol2.R . read.ncdf.R . read.pdb.R . read.pdb2.R . read.pdcBD.R . read.pqr.R . read.prmtop.R . rgyr.R . rle2.R . rmsd.R . rmsf.R . rmsip.R . rot.lsq.R . rtb.R . seq2aln.R . seqaln.R . seqaln.pair.R . seqbind.R . seqidentity.R . setup.ncore.R . sip.R . sse.bridges.R . store.atom.R . stride.R . struct.aln.R . summary.cna.R . summary.cnapath.R . summary.pdb.R . torsion.pdb.R . torsion.xyz.R . trim.mol2.R . trim.pdb.R . trim.pdbs.R . trim.xyz.R . unbound.R . uniprot.R . var.xyz.R . vec2resno.R . vmd.R . vmd.cna.R . vmd.cnapath.R . vmd_colors.R . wrap.tor.R . write.crd.R . write.fasta.R . write.mol2.R . write.ncdf.R . write.pdb.R . write.pir.R . write.pqr.R . xyz2atom.R . Full bio3d package functions and examples
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