Tag: Structural Model

Gen3D – 3D Genome and Chromosome Structural Model Construction

Gen3D

:: DESCRIPTION

Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Gen3D

:: MORE INFORMATION

Citation

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
Nowotny J, Ahmed S, Xu L, Oluwadare O, Chen H, Hensley N, Trieu T, Cao R, Cheng J.
BMC Bioinformatics. 2015 Oct 23;16(1):338.

ENSEMBLE – Generate Structural Models of the unfolded state

ENSEMBLE

:: DESCRIPTION

The ENSEMBLE suite contains tools to determine and analyze the weighted ensemble of structures that best represents the unfolded state within the boundaries of a pre-determined conformer pool. In order to do this, a weighted ensemble is used to represent the unfolded state as a collection of rigid structures, each associated with a numerical term proportional to the time-averaged existence of that particular conformation.

::DEVELOPER

Julie Forman-Kay’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ENSEMBLE

:: MORE INFORMATION

Citation

J Mol Biol. 2009 Aug 14;391(2):359-74. doi: 10.1016/j.jmb.2009.06.001. Epub 2009 Jun 6.
Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints.
Marsh JA, Forman-Kay JD.