We take action in the fight against COVID-19

NI4OS-Europe opens a fast track access channel to its services, tools and software for the Scientific communities that perform extensive research to tackle the COVID-19.

Computational resources have already been allocated to the Bioinformatics European Research Era Chair and the Bioinformatics Group at the Cyprus Institute of Neurology and Genetics. The research team has put their efforts in the multi-omic analysis and network-based integration towards a highly-informed decision regarding a short list of repurposed drugs and related to them natural products against COVID-19.

APPLY and gain Fast Track Access to NI4OS-Europe resources

We have established a Fast Access Channel on generic services -computational (HPC, Cloud), data analysing tools, storage services, etc., for COVID-19 research.

Are you a researcher, contributing in the fight against COVID-19? Seize the opportunity and make use of NI4OS Fast Access Channel! Contact us at: ni4os-europe-covid19@ni4os-europe.eu

ACCESS to Open Data and Computational Resources on COVID-19

The scientific community is relying on Open Science to support and accelerate the ongoing research on the COVID-19. The relevant research papers and underlying data are made available in open access, or they are freely available for the duration of the epidemic.

The available scientific results should meet the highest standards and they should be traceable, easily accessible to researchers, effectively shared, practical and actionable. Findings and conclusions should be scrutinized and adequately presented.
This NI4OS-Europe incentive on combatting COVID-19 is an effort in this direction, in which we all learn by doing.

NI4OS-Europe wiki on COVID-19

EXPLOIT Computational Resources

EXPLOIT thematic services

Offering to researches from NI4OS countries, but potentially also to other resources, for all who are working in COVID-19 related fields.

ChemBioServer

Used for filtering Virtual Screening results.
Features: (i) browse and visualize compounds along with their properties, (ii) filter chemical compounds for a variety of properties such as steric clashes and toxicity, (iii) apply perfect match substructure search, (iv) cluster compounds according to their physicochemical properties providing representative compounds for each cluster, (v) build custom compound mining pipelines and (vi) quantify through property graphs the top ranking compounds in drug discovery procedures. ChemBioServer allows for pre-processing of compounds prior to an in silico screen, as well as for post-processing of top-ranked molecules resulting from a docking exercise with the aim to increase the efficiency and the quality of compound selection that will pass to the experimental test phase.

ChemBioServer

FEPrepare | https://feprepare.vi-seem.eu

FEPrepare

FEPrepare is a tool, which automates the set-up procedure for performing NAMD/FEP simulations. ​Automating free energy perturbation calculations is a step forward to delivering high throughput calculations for accurate predictions of relative binding affinities before a compound is synthesized, and consequently save enormous time and cost.

FEPrepare

AFMM | https://afmm.vi-seem.eu

AFMM

Tool for force field parametrization to run MD simulations of drug like molecules.The method used fits the molecular mechanics potential function to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The program optimizes an initial parameter set (either pre-existing or using chemically-reasonable estimation) by iteratively changing them until the optimal fit with the reference set is obtained. By implementing a Monte Carlo-like algorithm to vary the parameters, the tedious task of manual parametrization is replaced by an efficient automated procedure. The program is best suited for optimization of small rigid molecules in a well-defined energy minimum, for which the harmonic approximation to the energy surface is appropriate for describing the intra-molecular degrees of freedom.

AFMM

Nanocrystal | https://nanocrystal.vi-seem.eu

Nanocrystal

Creates nanoparticle models as drug carriers from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user.

Nanocrystal

Latest news on NI4OS-Europe vs COVID-19

Latest news on NI4OS-Europe vs COVID-19