[AMBER] SIRAH 2.0: a finer taste in coarse-grained protiens

From: Matias Machado <mmachado.pasteur.edu.uy>
Date: Thu, 11 Oct 2018 12:17:17 -0300 (UYT)

Dear Amberites,

We are please to announce the release of SIRAH 2.0, a complete coarse-grained force field for biomolecules, running native on AMBER 14+. It contains parameters for proteins, DNA, lipids (DMPC), ions and solvent. It's very easy to use, just map and go!

This release brings major improvements to the former protein model, including a reviewed set of bonded and non-bonded parameters to better describe the conformational landscape and hydrophilic/hydrophobic balance of the residues.

The average accuracy of SIRAH 2.0 on AMBER (~3A) is comparable to high-resolution cryo-EM experiments, with a performance of 2.6 microseconds/day for a protein of 108 residues on a GTX 1080.

The preprint version of the submitted manuscript is available at BioRxiv [https://doi.org/10.1101/436774]

SIRAH 2.0 is freely available at [http://www.sirahff.com] together with tutorials and FAQs.

The group is now working on expanding the library of lipids and metallic ions (to be released in a month or so). Sugars are also on the way...

Stay tuned,


Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

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Received on Thu Oct 11 2018 - 08:30:02 PDT
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