Tag: Dimer

PREDDIMER – Prediction tool for an Ensemble of Transmembrane α-helical Dimer Conformations

PREDDIMER

:: DESCRIPTION

PREDDIMER reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices.

::DEVELOPER

Laboratory of biomolecular modeling.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 15;30(6):889-90. doi: 10.1093/bioinformatics/btt645.
PREDDIMER: a web server for prediction of transmembrane helical dimers.
Polyansky AA1, Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG.

CooperativeDimer – Analysis of Ligand Binding to Dimers

CooperativeDimer

:: DESCRIPTION

CooperativeDimer is a software developed in Mathematica for the analysis of the affinities and any cooperativity in ligand binding to a dimer (or other molecule containing two equivalent binding sites). The approach requires data on the fractional populations of all three species (apo, singly and doubly bound) such as may be obtained from mass spectrometry or NMR data.

::DEVELOPER

Mark A. Williams

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Mathematica

:: DOWNLOAD

  CooperativeDimer

:: MORE INFORMATION

Citation

Marcus J. Edwards, Mark A. Williams, Anthony Maxwell and Adam R. McKay (2011).
Mass spectrometry reveals the antibiotic simocyclinone D8 binds DNA gyrase in “bent over” conformation: evidence for positive coperativity.
Biochemistry. 2011 May 3;50(17):3432-40. Epub 2011 Apr 5.