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v2.4 (Version 2.4,
released November 2019)
Overview of new
features and enhancements
New facilities for sequence alignment using the ‘msa’ package
from Bioconductor or alternatively using the online server of the
European Bioinformatics Institute (EMBL-EBI) (and so a local MUSCLE
program is no longer a mandate).
A more robust sequence fetching function supporting both the
EMBL-EBI and NCBI (National Center for Biotechnology Information)
servers.
A new function for “core” detection using contact maps, new and
improved functions for processing protein structures and doing
structural network analysis.
More advanced system environment checking for automatically
locating essential external programs.
Other updates
We have also updated online vignettes and other documentations.
For a fine-grained list of changes, or to report a bug, please
consult:
For full install instructions see:
Major new/enhanced functions
- seqaln: Supports using ‘msa’ and the EMBL-EBI server to do sequence
alignment
- get.seq: More robust to fetch a large number of sequences and
supports EMBL-EBI and NCBI servers
- atom.select.pdbs: New function for atom selection of a ‘pdbs’
object
- core.cmap: New function for “core” residues detection using contact
maps
- chain.pdb: Supports inspection on peptide bond (C-N) length
- community.aln: Comparison of networks with different numbers of
nodes
- dccm.pca, dccm.xyz: Tidier interface by merging “lmi()” and
providing a new argument “method”
- core.find, dccm.nma, dm.xyz, nma.pdbs, pdbaln, pdbsplit,
read.fasta.pdb: Improved progress bar
- dssp.pdb, pdbaln, pymol.dccm, pymol.modes, pymol.pdbs, seqaln:
Exefile argument with OS dependent defaults
- rmsd, seqidentity: More sensible output by fetching row and column
names from input
Happy Bio3Ding!
v2.3 (Version 2.3,
released September 2016)
Overview of new
features and enhancements
New facilities for ensemble normal mode analysis (NMA) with
all-atom elastic network model (ENM) and Gaussian network model
(GNM).
Enhanced NMA calculations with the rotation-translation block
(RTB) method and the new “4-bead” coarse-grained ENM.
More efficient reading of large PDB files using Rcpp.
PDB annotation from the PFAM database.
More supported I/O file formats.
Other updates
We have also updated online vignettes and other documentations.
For a fine-grained list of changes, or to report a bug, please
consult:
For full install instructions see:
Major new/enhanced functions
- aanma: All-atom ENM normal mode analysis (with RTB and 4-bead ENM
supported)
- aanma.pdbs: Ensemble NMA with all-atom ENM
- gnm: Gaussian network model (GNM) calculations
- gnm.pdbs: Ensemble NMA with GNM
- dccm.gnm: Dynamical cross-correlation for GNM
- pdbs2sse: Retrieve SSE from pdbs object with appropriate residue
numbers for plotting
- mask.dccm: Produce a new DCCM object with selected atoms masked
- pdb.pfam: Function for PFAM annotation of PDB IDs
- pymol.pdbs: Builds a pymol session from a ‘pdbs’ object
- read.cif: Read a Protein Data Bank (mmCIF) coordinate file
- read.dssp: For reading existing DSSP output files
- read.stride: For reading existing STRIDE output files
- read.crd: Read a CHARMM CARD (CRD) or AMBER coordinate file
- read.prmtop: Read parameter and topology data from an AMBER PrmTop
file
- read.pdb: Use Rcpp to (more rapidly) read and parse PDB files
- read.pdb2: Renamed old read.pdb function
- plot.matrix.loadings: For plotting loadings obtained from
pca.array()
- community.aln: To align communities from two or more related
networks
- atom.select: Supports ‘insert’ identifier
- vmd.cna and vmd.cnapath: Renamed view.cna and view.cnapath
- pymol.dccm, pymol.modes, pymol.nma, and pymol.pca: Renamed view.xxx
functions
- plot.fasta: Improved plotting function for multiple sequence
alignment
- read.mol2, write.mol2, atom.select, trim, as.pdb: Read, write and
manipulate mol2 files with functions
Happy Bio3Ding!
v2.2 (Version 2.2,
released in Feb 2015)
Added new facilities for:
sub-optimal path analysis of biomolecular correlation
networks
constructing biological units
identification and tidying of malformed PDB files
improved secondary structure annotation of ‘pdbs’ objects and
various plots.
Other updates
We have also updated and enhanced atom selection functionality
and developed a new vignette detailing PDB structure manipulation and
analysis facilities. For a fine-grained list of changes, or to report a
bug, please consult:
Major new functions
- cnapath: Suboptimal Path Analysis for Correlation Networks
- biounit: Biological Unit Construction
- clean.pdb: Inspect And Clean Up A PDB Object
- cat.pdb: Concatenate Multiple PDB Objects
- pdb2sse: Obtain An SSE Sequence Vector From A PDB Object
- bounds.sse: Obtain A SSE Object From An SSE Sequence Vector
- aa.table: Updated amino acid reference data that replaces older
‘aa.mass’
- as.fasta: Convert alignment/sequence in matrix/vector format to a
FASTA object.
- as.pdb: Convert coordinate data to PDB format
- as.select: Convert atomic indices to a atom.select object
- as.xyz: Convert vectors and matrices to ‘xyz’ class objects
- atom.select.pdb: Atom selection from PDB objects has been
extensively updated
- basename.pdb: Utility for manipulation of PDB file names
- check.utility: Check and Report on Missing Bio3D Utility
Programs
- cmapt: Update contact map methods for pdb and xyz objects
- cna: Update correlation network analysis methods for dccm and ensmb
objects”
- cnapath: Suboptimal Path Analysis for Correlation Networks
- com: Updated center of mass methods for pdb and xyz objects
- combine.select: Combine atom.select objects, renamed from previous
‘combine.sel’
- cov.enma: New method to Calculate Covariance Matrix from Ensemble
Normal Modes”
- cov2dccm: Calculates the N-by-N cross-correlation matrix from a
3N-by-3N covariance matrix
- covsoverlap: New methods for nma and enma objects
- dm: Distance matrix gets new methods for pdb and xyz class
objects
- dssp: Secondary Structure Analysis with DSSP gets new methods for
pdb, xyz and pdbs class objects
- geostas: Geometrically stable domain finder gets new methods for
nma, enma, pdb, pdbs and xyz objects.
- is.pdbs: Is an Object of Class pdbs
- mono.colors: New color palette
- pdb2sse: Obtain An SSE Sequence Vector From A PDB Object
- pdbfit: Coordinate superposition gets new methods for multi-model
pdb objects and pdbs objects.
- read.crd: Can Now Read Coordinate Data from Amber or CHARMM
- read.prmtop: Read AMBER Parameter/Topology files
- var.pdbs: Pairwise Distance Variance in Cartesian Coordinates
- plot: New or updated plot methods for ‘cmap’, ‘geostas’, and ‘pca’
class objects as well as a new plot.fluct() function that expands on
plot.bio3d() for plotting atomic fluctuations from MD and NMA
results.
- print: New print methods for cnapath, enma, geostas, mol2, nma, pca,
pdb, prmtop, rle2, select and sse objects.
v2.1 (Version 2.1,
released in Sep 2014)
Overview of major changes
Added new facilities for correlation Network Analysis (cna) and
Geometrically Stable Domain finding (geostas).
We have also changed ‘PDB object data’ storage from a matrix to a
data.frame format.
Improved methods and functionality for ensemble NMA are now also
included along with extensive improvements to package vignettes and
function documentation. For a fine-grained list of changes, or to report
a bug, please consult:
Major new functions
- cna: Protein Dynamic Correlation Network Construction and Community
Analysis.
- plot.cna: Protein Structure Network Plots in 2D and 3D.
- print.cna: Summarize and Print Features of a cna Network Graph
- identify.cna: Identify Points in a CNA Protein Structure Network
Plot
- layout.cna: Protein Structure Network Layout
- view.cna: View CNA Protein Structure Network Community Output in
VMD
- prune.cna: Prune A cna Network Object
- community.tree: Reconstruction of the Girvan-Newman Community Tree
for a CNA Class Object.
- network.amendment: Amendment of a CNA Network According To A Input
Community Membership Vector.
- lmi: Linear Mutual Information Matrix
- dccm.pca: Dynamic Cross-Correlation from Principal Component
Analysis
- filter.dccm: Filter for Cross-correlation Matrices (Cij)
- cmap.filter: Contact Map Consensus Filtering
- geostas (amsm.xyz): GeoStaS Domain Finder
- bhattacharyya Bhattacharyya Coefficient
- covsoverlap: Covariance Overlap
- sip: Square Inner Product
- cov.nma: Calculate Covariance Matrix from Normal Modes
- mktrj.enma: Ensemble NMA Atomic Displacement Trajectory
- pca.array: Principal Component Analysis of an array of matrices
- hmmer: HMMER Sequence Search
- plot.hmmer: Plot a Summary of HMMER Hit Statistics.
- uniprot: Fetch UniProt Entry Data.
- pfam: Download Pfam FASTA Sequence Alignment
- hclustplot: Dendrogram with Clustering Annotation
- write.pir: Write PIR Formated Sequences
- mustang: Structure-based Sequence Alignment with MUSTANG
- pdbs.filter: Filter or Trim a pdbs PDBs Object
- dssp.pdbs: Secondary Structure Analysis of Aligned PDB Structures
with DSSP
- plot.fasta: Plot a Multiple Sequence Alignment
- print.fasta: Printing Sequence Alignments
- inspect.connectivity: Check the Connectivity of Protein
Structures
- var.xyz: Pairwise Distance Variance in Cartesian Coordinates
- is.xyz(as.xyz, print.xyz): Is an Object of Class
- setup.ncore: Setup for Running Bio3D Functions using Multiple CPU
Cores
v2.0 (Version 2.0,
released in Nov 2013)
Major new functions
- aa2mass: Amino Acid Residues to Mass Converter
- atom.index: Index of Atomic Masses
- atom2mass(atom2ele, formula2mass): Atom Names to Mass Converter
- binding.site: Binding Site Residues
- com(com.xyz): Center of Mass
- combine.sel: Combine Atom Selections From PDB Structure
- dccm.enma: Cross-Correlation for Ensemble NMA (eNMA)
- dccm.mean: Filter DCCM matrices
- dccm.nma: Dynamic Cross-Correlation from Normal Modes Analysis
- dccm.xyz: DCCM: Dynamical Cross-Correlation Matrix
- deformation.nma: Deformation Analysis
- dssp.trj: Secondary Structure Analysis of Trajectories with
DSSP
- fluct.nma: NMA Fluctuations
- inner.prod: Mass-weighted Inner Product
- is.pdb: Is an Object of Class pdb
- is.select: Is an Object of Class atom.select
- load.enmff(ff.calpha, ff.calphax, ff.anm, ff.pfanm, ff.sdenm,
ff.reach): ENM Force Field Loader
- mktrj.nma: NMA Atomic Displacement Trajectory
- nma(build.hessian, print.nma): Normal Mode Analysis
- nma.pdbs(print.enma): Ensemble Normal Mode Analysis
- normalize.vector: Mass-Weighted Normalized Vector
- pdb.annotate: Get Customizable Annotations From PDB
- pdb2aln: Align a PDB structure to an existing alignment
- pdb2aln.ind: Mapping between PDB atomic indices and alignment
positions
- pdbfit: PDB File Coordinate Superposition
- pdbs2pdb: PDBs to PDB Converter
- plot.enma: Plot eNMA Results
- plot.nma: Plot NMA Results
- plot.rmsip: Plot RMSIP Results
- read.mol2: Read MOL2 File
- sdENM: Index for the sdENM ff
- sse.bridges: SSE Backbone Hydrogen Bonding
- struct.aln: Structure Alignment Of Two PDB Files
- view.dccm: Visualization of Dynamic Cross-Correlation
- view.modes: Vector Field Visualization of Modes
- vmd.colors: Color as in VMD Molecular Viewer
Versioning
For
changes prior to v1.1-6 (Apr 2013) please see the bio3d wki:
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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