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bio3d

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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]

All associated links for this package

First Published: 2014-10-15

Latest Update: 2022-10-26

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 22 Dec. 2024.

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

View bio3d dependency map

Complete documentation for bio3d

View documentation PDF

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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