Structures

Here we will aim to keep an up-to-date list of important structures as they become available.

• The CompBioMed consortium has a good Covid-19 web page containing lots of link to high quality information link

• Diamond page for scientists working on Covid-19 (link) and rapid access for experimentalists to access facility resources (link)

• EMBL-EBI resource web page on Covid-19 link

• A useful how-to on building on SARS-CoV-2 fragment screens from the Diamond/XChem fragments link

• The latest SCOP2 release 2020-03-31 includes classifications for all PDB structures from SARS-CoV-2, as well as from related coronaviruses. This release provides the classification of 24 Coronavirus SARS-CoV-2 non-redundant domains representing 294 structures. link

• Tristan Croll (Cambridge) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Tristan has been working through and (where applicable) improving the existing experimental SARS-CoV-2 structures using ISOLDE (narrated via Twitter @crolltristan). Tristan is willing to share revised coordinates with whoever needs them and to help check/rebuild your target of interest link

• Michael Feig (Michigan State) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  We generated new predictions for non-homology SARS-CoV-2 protein structures. SARS-CoV-2 is the virus that causes COVID-19 link

• Andrea Thorn (Wuerzburg) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  The thorne group have formed a task force of structural biologists and have begun collecting structures link
  
  It can be used to download all relevant structures, look at structural validation information, diagnostic data for the quality of experimental data and available re-refinements. We will expand this resource in time,but as of today, it contains all deposited SARS-CoV and SARS-CoV-2 structures, sorted by protein and virus, PDB-REDO entries, diffraction data diagnostics from AUSPEX and PHENIX.XTRIAGE, WHATCHECK reports and Tristan Croll's fantastic manual ISOLDE re-refinements. We will soon add MOLPROBITY to lighten the traffic on the server at Duke, individual links to Global Phasing's efforts in re-processing and re-refinement of individual structures and HARUSPEX map annotations for the Cryo-EM structures.

• Alexandre Bonvin (Utrecht) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  

  The WeNMR/HADDOCK portal for the modelling of biomolecular interactions, developed at Utrecht University, has seen an increase of registrations over the last weeks with many users indicating they intend to use it for COVID-19 projects. HADDOCK is a core software in the BioExcel Center of Excellence, which has also committed to support COVID-19 researchers. The HADDOCK portal makes use of EGI/EOSC-Hub HTC resources.

  For this purpose, together with EGI/EOSC-Hub experts, the team has already expanded the processing capacity of the HADDOCK portals. The new HADDOCK2.4 portal allows users to flag their runs as COVID-19 related. Additional HTC resources are being added to the sites already supporting WeNMR, in particular we expect soon to have support from the US Open Science Grid. Further the team is looking into deploying customized solutions to support researchers. These might take the form of dedicated virtual clusters with a HADDOCK frontend running on EOSC cloud resource, and customized virtual machines with ready to run local HADDOCK installation for experienced users wanting to use the software at the command line.

  Next to providing increased resources to researchers, the HADDOCK team is also running a number of COVID-19 projects and is involved in collaborations ranging from drug screening against the protease to modelling COVID-19 related protein-protein interactions.

• The UCSC Genome Browser have made a comprehensive list of information available, read more with links here.

• An initiative run by the biomolecular simulations group at Institut Pasteur de Montivideo to create 10ms+ trajectories of coarse grained systems and depositing them on zenodo link

People

Groups willing to run simulations

• Michelle Sahai This email address is being protected from spambots. You need JavaScript enabled to view it. (Roehampton)
  
  Can help with MD simulations (ACEMD and NAMD), Docking, analyses, ligand parameterisation (HTMD Parameterize for AMBER and CHARMM force fields)

• Christof Jaeger (Nottingham) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  The Protein Engineering team are willing to offer experienced modelling hands for help in simulation setup and in analytical techniques (scripting, coding, chemical knowledge etc) along with access to some of their local compute resources which comprise of some CPU and ~10 GPUs of varying ages (GTX series to V100). They are also willing to act as a point of introduction into the IBM community grid (BOINC) to access resources of upto 750K volunteers (lead times may be longer).

• Andrei Pisliakov group (Dundee) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Can help with MD simulations.

• Syma Khalid group (Southampton) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Can help with atomistic and coarse grained MD simulations, analyses (GROMACS, NAMD).

• Dan T Major group (Bar-Ilan) This email address is being protected from spambots. You need JavaScript enabled to view it. group website
  
  We can contribute with our EnzyDock approach and general enzymatic theory work and docking.

• Jacob Swadling (PDRA, LMRC Cambridge)

• Sarah Harris group (Leeds) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Can help with MD simulations, docking, analyses, ligand parameterisation (AMBER).

• Phill Stansfeld group (Warwick) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Can help with atomistic and coarse grained MD simulations and analyses.

• Jon Essex group (Southampton) This email address is being protected from spambots. You need JavaScript enabled to view it. 
  
  Can help with molecular dynamics, monte carlo, docking.

• Martyn Winn group (STFC DL and RAL) This email address is being protected from spambots. You need JavaScript enabled to view it. 
  
  Can help with experimental structure determination and analysis of targets, docking, MD simulations, free energies.

• Elisa Frezza group (Paris Descartes) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Can help with MD simulations using GROMACS (mostly all-atom, but also coarse-grain using MARTINI), ligand parametrization for AMBER force field (AMBER and GROMACS softwares), analyses, normal mode analysis and some calculations with PLUMED (like Halmitonian Replica Exchange).
  
  Elisa has access to compute resource for this effort via a light touch application process.

• Mary J Ondrechen group (Northeastern University) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  My research group and I are working on coronavirus protein structures. We have a unique technique for predicting druggable sites, including catalytic, allosteric, and other interaction sites in protein structures. We are performing site predictions and docking simulations and have other capabilities including MD and protein electrostatics.

• Stephen Wells (Bath) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  I work on geometric modelling of protein flexibility. I put out a preprint last week on bioRxiv in which I show how the global flexibility of the protein affects binding-site geometries in a viral protease. I can do a similar study on any other viral protein structure if this would help with structure-based drug design efforts.

• Michael Sternberg (Imperial) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Missense3D - models the effect of a missense variant in a protein structure and we can apply it in batch including model protein/protein interfaces link
  
  PhyreRisk – A dynamic database facilitating mapping genetic variants onto experimental and predicted human protein structures link
  
  Phyre2 – Protein structure prediction including batch processing link

• Franck Jolibois and Adrien Schahl (Paul Sabatier University - Toulouse III) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  On our side, we can help with classical molecular dynamics (NAMD, AMBER, GLYCAM), charge development (DFT at the HF level, similar to the RESP method) and spectroscopy calculations (DFT at HF, B3LYP and others level of calculations). If needed, we can also perform reactivity calculation using DFT.

• Matteo Salvalaglio (UCL) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  Our expertise is in the application of molecular dynamics and enhanced sampling methods (metadynamics, umbrella sampling) to obtain thermodynamic and kinetic information on molecular processes (in particular nucleation, crystal growth and conformational transitions). We can help with atomistic MD, metadynamics simulations, and trajectory analysis.

• Giovanni Bottegoni (Birmingham) This email address is being protected from spambots. You need JavaScript enabled to view it.
  
  We could contribute to drug discovery efforts with our expertise in in silico polypharmacology - computer-assisted identification of multi-target directed ligands. We have also worked on several MTDL discovery projects involving covalent interactions at at least one of the sought targets (see for example De Simone et al., J Med Chem 2017)

HPC

Please contact This email address is being protected from spambots. You need JavaScript enabled to view it.

PRACE has opened a flash call for researchers working on Covid-19 related research link

IBM and DOE launch large Covid-19 computing consortium link