Changes in version 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! Changes in version 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! Changes in version 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. Changes in version 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 Changes in version 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: - .- - 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/. Changes in version 1.1-6