PDIviz 1.2.3 – Visualization of Protein-DNA Binding Interfaces

PDIviz 1.2.3

:: DESCRIPTION

PDIviz is a plugin for the PyMOL molecular visualization system that is specifically designed to visualize protein-DNA interfaces in three dimensions. PDIviz detects the interface of protein-DNA complexes by calculating the buried surface area directly in PyMOL.

::DEVELOPER

MBL – Laboratorio de Bioinformática

:: SCREENSHOTS

PDIviz

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • PyMOL

:: DOWNLOAD

  PDIviz

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 16. pii: btv203.
PDIviz: Analysis and visualization of protein-DNA binding interfaces.
Ribeiro J, Melo F, Schüller A

MixChIP – Cell Type Specific Protein-DNA Binding analysis

MixChIP

:: DESCRIPTION

MixChIP is a probabilistic method for identifying cell type specific TF binding sites from heterogeneous chromatin immunoprecipitation sequencing (ChIP-seq) data.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 MixChIP

:: MORE INFORMATION

Citation

MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis.
Rautio S, Lähdesmäki H.
BMC Bioinformatics. 2015 Dec 24;16(1):413. doi: 10.1186/s12859-015-0834-3.

SparScape – Predicting Sparse protein-DNA binding Landscapes

SparScape

:: DESCRIPTION

SparScape is a penalized Bayesian approach to predicting sparse protein-DNA binding landscapes.

::DEVELOPER

Matthew LevinsonQing Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/

:: DOWNLOAD

 SparScape

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):636-43. doi: 10.1093/bioinformatics/btt585. Epub 2013 Oct 9.
A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes.
Levinson M1, Zhou Q.