HTMD: High-throughput molecular dynamics

HTMD is a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems. HTMD is based on Python, so scientists can easily extend it to their needs. With HTMD is possible to do very complex protocols in just few lines.

In a single script, it is possible to plan an entire computational experiment, from manipulating PDBs, building, executing and analyzing simulations, computing Markov state models, kinetic rates, affinities and pathways.

HTMD has been successfully used for FBDD, for GPCR ligand binding, Antibody structural analysis and more.
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HTMD main features such as Markov state analysis and molecular dynamics

HTMD


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Download HTMD to prepare and analyze MD.

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Distinctive Features



References

S. Doerr , M.J. Harvey, F. Noé ,G. De Fabritiis, HTMD: High-throughput molecular dynamics for molecular discovery, J Chem Theory Comput. 12(4), pp1845-1852 (2016)

N. Stanley and G. De Fabritiis, High throughput molecular dynamics for drug discovery, In Silico Pharmacology, 3:3 (2015)

S. Doerr and G. De Fabritiis, On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations, J. Chem. Theory Comput. 10 (5), pp 2064–2069(2014)