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:
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:
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:
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)
Contains over 30 new functions including enhanced Normal Mode
Analysis facilities as well extensive improvements to existing code and
documentation. For a fine-grained list of changes or to report a bug,
please consult: