SIRAH – Mapping, Backmapping and Visualization of Coarse-grained Models

SIRAH

:: DESCRIPTION

SIRAH Tools (Southamerican Initiative for a Rapid and Accurate Hamiltonian) comprises a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the SIRAH force field.

::DEVELOPER

SIRAH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • AMBER/ GROMACS

:: DOWNLOAD

 SIRAH

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Jan 14. pii: btw020.
SIRAH Tools: mapping, backmapping and visualization of coarse-grained models.
Machado M, Pantano S

CG2AA – Backmapping Protein Coarse-Grained Structures

CG2AA

:: DESCRIPTION

CG2AA is a computer program that accurately reconstructs the atomistic structure from CG models from the force field developed in (Hills et al., 2010), using a simple geometrical algorithm.

::DEVELOPER

CG2AA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

  CG2AA

:: MORE INFORMATION

Citation

CG2AA: Backmapping Protein Coarse-Grained Structures.
Lombardi LE, Martí MA, Capece L.
Bioinformatics. 2015 Dec 16. pii: btv740.