NEWS

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bio3d 2.4

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:

  • The issues log
  • The commit log

• For full install instructions see:

  • http://thegrantlab.org/bio3d/articles/online/install_vignette/Bio3D_install.html

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!

bio3d 2.3

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:

  • The issues log
  • The commit log

• For full install instructions see:

  • http://thegrantlab.org/bio3d/articles/online/install_vignette/Bio3D_install.html

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!

bio3d 2.2

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:

  • The issues log
  • The commit log

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.

bio3d 2.1

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:

  • The issues log
  • The commit log

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

bio3d 2.0

• 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:

  • The issues log
  • The commit log

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

• Releases will be numbered with the following semantic versioning format:

  • <major>.<minor>-<patch>

  • E.g.: 2.0-1

• And constructed with the following guidelines:

  • Breaking backward compatibility bumps the major (and resets the minor and patch)
  • New additions without breaking backward compatibility bumps the minor (and resets the patch)
  • Bug fixes and misc changes bumps the patch

For more information on SemVer, please visit http://semver.org/.

bio3d 1.1-6

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