Technologies

PELEplat

Packages BACK

This is our integrated platform with a variety of features supporting:

nbd-technologies-pele-simulation-platform

Induced Fit

The induced fit simulation aims to enhance docking poses by taking into account the receptor flexibility, it is achieved by our curated ligand perturbation, side chain prediction and backbone rearrangement though normal modes, which have been benchmarked extensively.

Pocket Exploration

The Pocket Exploration tool explores the whole protein surface to obtain putative binding modes of your small molecule and retrieve the most promising binding sites of your receptor.

PPI

Protein-Protein Interaction package explores the interface between two protein domains, retrieves potential binding sites and then refines the position by performing a short minimization.

GPCR

GPCR package to elucidate the binding mode of a small molecule to the orthosteric site of a G protein-coupled receptor. Once the user specifies the initial and orthosteric sites, PELE Platform will automatically create the simulation box and add constraints on the α-carbons to prevent the collapse of the structure due to the lack of membrane.

Out → In

The Out → In simulation aims to find the binding/unbinding paths of a small molecule to a given receptor while opening the pocket, useful in cases where no grid can be found with docking algorithms, or when aiming to elucidate migration pathways.

FragPELE

This package is capable of performing high-throughput fragment growing onto a scaffold while exploring the protein-ligand conformational space. Aims to rank congeneric series as well as discover cryptic pockets and novel interactions due to rearrangements of the pocket.

Rescoring

This package aims to score and rank several putative poses. It is automatically run at the end of any other packages to prioritize the binding modes found along the simulation.

DirectEvolutionPELE

Accurately assess the binding and diffusion of your substrate to hundreds of enzyme variants within less than a week. Rank them accordingly to your own criteria.

PELE-DNA

PELE-DNA aims to accurately predict your DNA or RNA interaction with small molecules (intercalation, etc.). Combined with pyDock, we can also simulate your DNA.RNA -protein binding modes.

RECENT UPDATES & NEW FEATURES

AquaPELE

AquaPELE extends the exploration capabilities while keeping efficiency as it employs a mixed implicit/explicit approach to take into account the effects of buried water molecules. With an additional Monte Carlo routine, a set of explicit water molecules is perturbed inside protein cavities and their effects are dynamically adjusted to the current state of the system. As a result, this implementation can be used to predict the principal hydration sites or the rearrangement and displacement of conserved water molecules upon the binding of a ligand.


Conformation Change

In this simulation we apply a slight bias in order to find a binding mode containing a specific interaction between two user-defined atoms.


PluriZymePELE

Find putative binding sites within your current enzyme, mutate them to have your catalytic triad and obtain the new enzyme with the best combinations of mutations to produce a newly fully functional catalytic site.


Thermostability

From long Molecular Dynamics a centrality analysis will isolate relevant regions with high-flexibility with low conservation and without structural and functional relevance in an enzyme. Those positions will be mutated to all possible amino acids and delta-delta-G will be calculated with different functions, creating a consensus function to score the most stabilizing mutations.