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.
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:
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.
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:
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.
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:
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:
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:
Releases will be numbered with the following semantic versioning format:
<major>.<minor>-<patch>
E.g.: 2.0-1
And constructed with the following guidelines: