Nothing
##"io"
sd_section("Input/Output:",
"Read and Write Common Biomolecular Data Types",
c(
"read.pdb",
"read.fasta",
"read.fasta.pdb",
"read.ncdf",
"read.dcd",
"read.crd",
"read.pqr",
"read.mol2",
"read.all",
"read.pdcBD",
"read.cif",
"read.crd.amber",
"read.crd.charmm",
"read.prmtop",
"aln2html",
"get.pdb",
"get.seq",
"load.enmff",
"write.pdb",
"write.crd",
"write.fasta",
"write.ncdf",
"write.pqr",
"write.pir",
"write.mol2",
"mktrj.nma",
"mktrj.pca",
"mktrj.enma",
"pymol",
"vmd"
)
)
##"sequence"
sd_section("Sequence Analysis:",
"Do Interesting Things with Protein Sequence",
c(
"consensus",
"conserv",
"blast.pdb",
"hmmer",
"pfam",
"uniprot",
"entropy",
"filter.identity",
"seqidentity",
"motif.find",
"pdbaln",
"seq2aln",
"seqaln",
"seqaln.pair",
"seqbind"
)
)
##"structure"
sd_section("Structure Analysis:",
"Do Interesting Things with Protein Structure",
c(
"angle.xyz",
"biounit",
"blast.pdb",
"get.blast",
"atom.select",
"combine.select",
"cmap",
"filter.cmap",
"core.find",
"core.cmap",
"com",
"dccm",
"filter.dccm",
"dist.xyz",
"dm",
"dssp",
"dssp.pdbs",
"geostas",
"mustang",
"fit.xyz",
"binding.site",
"mktrj",
"mktrj.pca",
"overlap",
"pca",
"pca.xyz",
"pca.pdbs",
"pca.array",
"pca.tor",
"dccm.pca",
"project.pca",
"pdbaln",
"pdb.annotate",
"pdb2aln",
"pdb2aln.ind",
"pdb2sse",
"pdbs2sse",
"pdbfit",
"chain.pdb",
"convert.pdb",
"rgyr",
"rmsd",
"filter.rmsd",
"rmsf",
"rmsip",
"struct.aln",
"torsion.pdb",
"torsion.xyz",
"wrap.tor",
"aa2mass",
"aa.table",
"atom.index",
"atom2mass",
"atom2ele",
"cov.nma",
"dccm.enma",
"dccm.nma",
"dccm.xyz",
"deformation.nma",
"fluct.nma",
"inner.prod",
"load.enmff",
"mktrj.nma",
"nma",
"nma.pdb",
"nma.pdbs",
"normalize.vector",
"pdbs2pdb",
"plot.enma",
"plot.nma",
"plot.rmsip",
"sdENM",
"sse.bridges",
"view.dccm",
"view.modes",
"var.xyz",
"inspect.connectivity"
)
)
##"trajectory"
sd_section("Trajectory Analysis:",
"Do Interesting Things with Simulation Data",
c(
"angle.xyz",
"cmap",
"filter.cmap",
"core.find",
"core.map",
"dccm",
"dccm.pca",
"filter.dccm",
# "lmi",
"dist.xyz",
"dm",
"dssp.xyz",
"geostas",
"fit.xyz",
"mktrj",
"mktrj.pca",
"overlap",
"project.pca",
"pca.tor",
"pca.xyz",
"pdbaln",
"rgyr",
"rmsd",
"filter.rmsd",
"rmsf",
"rmsip",
"torsion.pdb",
"torsion.xyz",
"wrap.tor"
)
)
##"nma"
sd_section("Normal Mode Analysis:",
"Probe Large-Scale Protein Motions",
c(
"aa2mass",
"aa.table",
"atom.index",
"atom2mass",
"atom2ele",
"bhattacharyya",
"cov.nma",
"covsoverlap",
"dccm.enma",
"dccm.nma",
"dccm.xyz",
"deformation.nma",
"geostas",
"fluct.nma",
"inner.prod",
"load.enmff",
"mktrj",
"mktrj.nma",
"mktrj.enma",
"nma",
"nma.pdb",
"nma.pdbs",
"aanma",
"aanma.pdbs",
"gnm",
"dccm.gnm",
"normalize.vector",
"pdbs2pdb",
"plot.enma",
"plot.nma",
"plot.rmsip",
"sdENM",
"sse.bridges",
"sip",
"var.xyz",
"var.pdbs",
"view.dccm",
"view.modes"
)
)
##"cna"
sd_section("Correlation Network Analysis:",
"Network analysis of dynamic coupling",
c(
"cna",
"cnapath",
# "cov2dccm",
"dccm",
# "lmi",
"filter.dccm",
"cmap",
"community.tree",
"network.amendment",
"view.cna",
"view.dccm",
"view.cnapath",
"plot.cna",
"print.cna",
"identify.cna",
"layout.cna",
"prune.cna",
"community.aln"
)
)
##"graphics"
sd_section("Graphics:",
"Plotting and Graphic Display",
c(
"bwr.colors",
"vmd_colors",
"mono.colors",
"plot.bio3d",
"plot.blast",
"plot.cmap",
"plot.core",
"plot.dccm",
"plot.dmat",
"plot.fluct",
"plot.geostas",
"plot.pca",
"plot.pca.loadings",
"hclustplot",
"plot.cna",
"plot.fasta",
"plot.hmmer",
"plot.matrix.loadings"
)
)
##"util"
sd_section("Utilities:",
"Convert and Manipulate Data",
c(
"aa.index",
"aa123",
"aa2index",
"aln2html",
"as.fasta",
"as.pdb",
"as.select",
"as.xyz",
"atom.select",
"combine.select",
"atom2xyz",
"basename.pdb",
"bio3d-package",
"biounit",
"bounds",
"bounds.sse",
"cat.pdb",
"check.utility",
"clean.pdb",
"chain.pdb",
"convert.pdb",
"diag.ind",
"difference.vector",
"gap.inspect",
"get.blast",
"inspect.connectivity",
"filter.identity",
"is.gap",
"is.pdb",
"is.select",
"is.xyz",
"is.pdbs",
"is.mol2",
"lbio3d",
"mask",
"orient.pdb",
"pairwise",
"plot.bio3d",
"print.core",
"print.cna",
"print.fasta",
"print.xyz",
"print.cnapath",
"print.enma",
"print.geostas",
"print.mol2",
"print.nma",
"print.pca",
"print.pdb",
"print.prmtop",
"print.rle2",
"print.select",
"print.sse",
"rle2",
"filter.rmsd",
"pdbseq",
"seqbind",
"pdbsplit",
"store.atom",
"trim",
"trim.mol2",
"trim.pdbs",
"trim.xyz",
"unbound",
"vec2resno",
"setup.ncore",
"elements",
"formula2mass"
)
)
##"example"
sd_section("Example Data:",
"Bio3d Example Data",
c("example.data")
)
#sd_icon("Some title:",
# "some sub-text",
# c("pants")
# )
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.