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The τRAMD (τ-Random Acceleration Molecular Dynamics) technique makes use of RAMD simulations to compute relative residence times (or dissociation rates) of protein-ligand complexes. In the RAMD method, the egress of a small molecule from a target receptor is accelerated by the application of an adaptive randomly oriented force on the ligand. This enables ligand egress events to be observed in short, nanosecond timescale simulations without imposing any bias regarding the ligand egress route taken. Apart from the estimation of relative residence times, the τRAMD method can be used to investigate dissociation mechanisms and characterize transition states by analysing the RAMD trajectories with the MD-IFP (Molecular Dynamics - Interaction Fingerprint) tool. The combined use of τRAMD and MD-IFP may assist the early stages of drug discovery campaigns for the design of new molecules or ligand optimization.

Other software

All software

3DSpineMFE

A MATLAB® toolbox that given a three-dimensional spine reconstruction computes a set of characteristic morphological measures that unequivocally determine the spine shape.

Modelling and simulation

Arbor

Arbor is a high-performance library for computational neuroscience simulations with multi-compartment, morphologically-detailed cells, from single cell models to very large networks. Arbor is written from the ground up with many-cpu and gpu architectures in mind, to help neuroscientists effectively use contemporary and future HPC systems to meet their simulation needs. Arbor supports NVIDIA and AMD GPUs as well as explicit vectorization on CPUs from Intel (AVX, AVX2 and AVX512) and ARM (Neon and SVE). When coupled with low memory overheads, this makes Arbor an order of magnitude faster than the most widely-used comparable simulation software. Arbor is open source and openly developed, and we use development practices such as unit testing, continuous integration, and validation.

Modelling and simulationCellular level simulation

BioExcel Building Blocks

BioExcel Building Blocks Workflows is a collection of biomolecular workflows to explore the flexibility and dynamics of macromolecules, including signal transduction proteins or molecules related to the Central Nervous System. Molecular dynamics setup for protein and protein-ligand complexes are examples of workflows available as Jupyter Notebooks. The workflows are built using the BioBB software library, developed in the framework of the BioExcel Centre of Excellence. BioBBis a collection of Python wrappers on top of popular biomolecular simulation tools, offering a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows.

Modelling and simulationMolecular and subcellular simulation

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