Acellera Ltd

The vision of Acellera is to transform the currently experimental driven process of drug design into a computerized driven process including both molecular simulations and innovative artificial intelligence methods.

We aim to be your partner during this transition. On the last decade, our team has acquired a strong expertise in these fields and has developed innovative tools -such as ACEMD, HTMD or AceCloud- which are based on state of the art technologies (GPU, Cloud Computing, Machine Learning and Neural Networks) to understand target conformational change, ligand interactions, optimise screening and optimise hit and lead.

Benefit from our know-how and open new perspectives for your Drug Discovery projects.

Understand protein-ligand interactions with all atom resolution using our high-throughput molecular dynamics technology. Obtain binding poses, kinetics, binding affinities and binding pathways for your compounds of choice.

Probe the binding properties of your fragment hits. Understand their binding pose, and affinity, as well as the specificity and selectivity of the interactions between the ligands and the target receptor.

The deliverables are:

• Target conformational space study
• Binding site discovery
• Binding pose determination
• Thermodynamics of binding, dG
• Kinetics of binding, kon/koff
• Video reports

This platform for small molecule discovery is unique in that it can assign binding site (including selectivity of binding and specificity of the intereaction), and pose (of binding and any metastable states) thanks to the simulation speeds we can obtain with Metrocubo, and the skills we are developing in data analysis. No other platform can give such complete data sets, which we can also help validate experimentally via NMR. This information can be invaluable for generating high affinity compounds for any target. In fact, there are many success stories in pharma relating the power of fragment based approaches for drug discovery.

On-demand molecular dynamics simulations service on our AceCloud infrastructure. Obtain up to a millisecond of molecular dynamics (MD) data using our patent-pending AceCloud compute infrastructure. Data analysis assistance is optional.
We prepare the inputs files, run the simulations and deliver the trajectories

Conformational Analysis & pocket detection

Determine the conformer space of biomolecule including small peptide, nucleic acid, carbohydrate or larger target protein in terms of their kinetic and thermodynamic fingerprints. Detect new pocket (allosteric, cryptic). Determine structures compatible with NMR data.

Metrocubo is a highly compact hardware-software solution for running GPU accelerated operations. That includes both molecular dynamics simulations and machine learning problems. Metrocubo GPU hardware delivers the highest teraflops per dollar ratio and offers your organization an efficient entry into the era of desktop high-throughput molecular dynamics simulations and artificial intelligence. Can be customised on demand

Molecular dynamics simulations are no longer limited by your in-house compute resources. With AceCloud, you can easily run cloud molecular dynamics simulations with any number of concurrent runs (two to hundreds) on Amazon Web Services (AWS) .

AceCloud minimizes the learning curve associated with cloud computing as its interface abstracts all interactions with the supporting cloud computing infrastructure. It emulates the experience of running cloud molecular dynamics locally on one’s own machine.

This software provides transparent execution of ACEMD (Amber, Charmm inputs) and Gromacs MD simulations. It has a built in mechanism by which the user may run arbitrary code (such as NAMD and Amber) on an AceCloud instance.

AceCloud complies with the major industrial security standards.

HTMD is a customizable molecular-specific programmable environment to prepare, handle, simulate, visualize and analyse 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 analysing 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.