Tag: Conformational Transition

GOdMD – Conformational Transitions with discrete Molecular Dynamics

GOdMD

:: DESCRIPTION

GOdMD is a new method for determining pathways for conformational transitions in macromolecules based on the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques.

::DEVELOPER

Molecular Modeling and Bioinformatics Unit , IRB Barcelona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):1980-6. doi: 10.1093/bioinformatics/btt324. Epub 2013 Jun 5.
Exploration of conformational transition pathways from coarse-grained simulations.
Sfriso P1, Hospital A, Emperador A, Orozco M.

NMSim – Modeling Macromolecular Conformational Transitions

NMSim

:: DESCRIPTION

NMSim is a normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W310-6. doi: 10.1093/nar/gks478. Epub 2012 Jun 4.
NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.
Krüger DM1, Ahmed A, Gohlke H.