Version 2.1, released in Sep 2014, contains 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 include:
- 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