Tag: Packing

SOCKET 3.03 / iSocket 0.3.1 – Identifies Knobs-into-holes packing in Protein Structures

SOCKET 3.03 / iSocket 0.3.1

:: DESCRIPTION

The SOCKET program finds the Knobs-into-Holes mode of packing between alpha-helices which is characteristic of coiled coils. It unambiguously defines the beginning and end of coiled-coil motifs in protein structures and assigns a heptad register to the sequence, highlighting the core-residues with a RasMol script if required.

iSocket is a set of computational tools written in Python as an add-on to the ISAMBARD software suite.

::DEVELOPER

WOOLFSON lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler / Python

:: DOWNLOAD

 SOCKET / iSocket

:: MORE INFORMATION

Citation

Heal JW, Bartlett GJ, Wood CW, Thomson AR, Woolfson DN.
Applying graph theory to protein structures: an Atlas of coiled coils.
Bioinformatics. 2018 Oct 1;34(19):3316-3323. doi: 10.1093/bioinformatics/bty347. PMID: 29722888; PMCID: PMC6157074.

Walshaw, J. & Woolfson, D.N. (2001)
Socket: a program for identifying and analysing coiled-coil motifs within protein structures.
J. Mol. Biol., 307 (5), 1427-1450

Voronoia 1.0 – Analyse Packing of Protein Structures

Voronoia 1.0

:: DESCRIPTION

Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins.

::DEVELOPER

Charité Berlin – Structural Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Voronoia

:: MORE INFORMATION

Citation

Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R.
Voronoia: analyzing packing in protein structures.
Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5.