A great paper (https://rdcu.be/ecxKI) from the group of Prof. Buckle explaining why Ab can recognize GAD65 but does not recognize GAD67. Also, this highlight (again) that upon brigand-binding, proteins become more stable.
In addition, this paper is a beautiful example of how to combine experimental and theoretical methods for the use of proteins function or dysfunction.

I am shamefully copying this post from Linkedin but if you happen to know any candidate, do not hesitate to reach:

It's on. To my #ComputationalChemistry network, I am calling on you.

The PM2E team in the CIMAP laboratory (www.cimap.ensicaen.fr) is looking for a #PhD hashtag#candidate. The goal of the project is to understand key parameters in #semiconductor defects stability and physics (both vacancies and color centers, see for example: https://doi.org/10.1016/j.nimb.2022.12.025) through the use of
#DFT and #MolecularModeling. The end goals of the project is concerned with application for #QuantumComputing through the making of stable #qubit. Collaboration and communication with experimentalists will be part of the project.

If you're interested in #MolecularDynamics, #MonteCarlo simulations, or DFT and quantum calculations, we are waiting for you. We are using codes such as #Lammps and #QuantumEspresso. We are looking for a candidate finishing or already having a master degree (or equivalent diploma) with training in #physics/ #MaterialsScience / #TheoreticalChemistry. Any experience in programming using #Python, #C and the #Linux environment would be considered a plus.

The position is located in Alençon (Orne) between Caen and Le Mans. Founding is assured for relevant candidates.

Link to the offer (in french, you can ask for an english version): https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs

Trying to get back in the #moleculardynamics bandwagon. Found a #NMR structure for a relatively small neurotoxin protein bound to a small peptide that neutralizes it. No one seems to have done any MD simulations yet. Started some sims. Maybe I’ll observe something interesting worth publishing.

Thrilled to share our new paper in PROTEINS! "Similar but Distinct-Biochemical Characterization of Staphylococcus aureus Serine Hydrolases FphH and FphI" (https://doi.org/10.1002/prot.26785) reveals key structural features of these enzymes, including flexible lids and distinct active sites. My MD simulations contributed to this work, led by Matthias Fellner. This research advances our understanding of S. aureus biofilm formation and could lead to targeted therapies.
#ProteinScience
#MolecularDynamics

Is anyone doing structure prediction with #AlphaFold3 figured out an easy way to do the relaxation step that Colabfold did? I'm looking into OpenMM and Amber, and making some progress, but it seems like it will be very difficult to make it work when phosphoresidues, ions, or anything else besides standard amino acid residues are included.

In-Situ Techniques on GPU-Accelerated Data-Intensive Applications

#CUDA #HPC #Performance #MolecularDynamics

https://hgpu.org/?p=29336

RBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit

#CUDA #MolecularDynamics #Physics #Package

https://hgpu.org/?p=29302

Para los que estuvieron en mi charla en la FLISoL sobre clústers de cálculo numérico, hoy largamos 729 simulaciones de 3000 partículas al clúster de una, más o menos esperamos que el mismo complete 10 corridas por día, por lo que en unos 73 días tendríamos los resultados #hpc #cluster #ciencia #md #dinamicamolecular #moleculardynamics #science #fisica #physics