Search Results for "dssp"

We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and...

...The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/

SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only Cα, ...) 3. Evaluate statistical distributions of internal variables: a. single variable distributions (including the most relevant in the atomistic representation, e.g. PHI and PSI and a number of those for the Cα based representation) b. two variables correlations (including the PHI-PSI Ramachandran map and its equivalent in the Cα based representation) c. three variables correlations

A set of object-oriented Perl tools for working with protein structure data, and integrating stand-alone tools such as dssp. See also pdbperl.net (soon to appear...) This code is still in very developmental stages, any contributions most welcome.