Mohammad ElGamacy

[Mohammad ElGamacy @m_elgamacy]

By manipulating the receptors association geometry, we managed to induce biased, and more selective, signaling along the G-CSF axis.

paper: https://t.co/7YdRUi0RXK

[Mohammad ElGamacy @m_elgamacy]

The HECTOR method is now out, where starting from maximal steric complementarity could achieve high-affinity binders, with experimental validation against VEGF and IL-7Ra as targets.

paper: https://t.co/AVBHIyEG9X
code: https://t.co/KMH5OL3frj

[Mohammad ElGamacy @m_elgamacy]

@_hcg_ Is the released version of CAPE-MPNN still optimized for only the presented 6 MHC-I alleles in the paper, or did you cover more variants later?

[Mohammad ElGamacy @m_elgamacy]

@AllThingsApx Yeah, it is stable for over 700 ps!

[Christopher W. Wood @ChrisWellsWood]

Our paper on the Protein Design Archive has just been published in @NatureBiotech! It describes our web application for exploring designed proteins (link ⬇️) and contains analysis of how they have changed over time. @MartaChronowska @mjstam @WoolfsonLab
https://t.co/7aa50oYRqQ

[Mohammad ElGamacy @m_elgamacy]

@aarondfrancis Probably incomplete code, and no linux 😔

[Damietta Protein Design Toolkit @proteintoolkit]

D-amino acids are now available in all design and MD protocols, on standalone and server software.

The table of valid input 3-letter codes: https://t.co/Hn302sFSto

[PLOS Biology @PLOSBiology]

Blocking cytokine signaling can be an effective therapy for a range of different diseases. @m_elgamacy &co use computational protein design to develop novel #cytokine receptor antagonists, showing G-CSFR inhibition in a cell model of AML #PLOSBiology https://t.co/artoueBUEL

[Mohammad ElGamacy @m_elgamacy]

We have an available PhD project in our group as part of this round of the IMPRS:

https://t.co/9ZFlnIulLP

[Mohammad ElGamacy @m_elgamacy]

By designing bivalent binders that lock a cytokine receptor into a non-signaling assembly, Timo has managed to create the most potent (and most stable) G-CSFR antagonists to date!

For details: https://t.co/hRhO4ssx4W

[Joana Pereira @Joana_MPereira]

📢The future Pereira lab is hiring! We will start at @_VIB_AI in February 2025 and are looking for a postdoc to join and kick-start our team 🤓 If you want to leverage AI and large networks to explore and understand the protein universe 🌌, check below! https://t.co/R7n5vam6mS

[Mohammad ElGamacy @m_elgamacy]

We have up to three HiWi (1 year contract) and/or Master's thesis projects in Tuebingen on topics of: i) deimmunization of synthetic cytokines, ii) Optimization of metal-binding proteins, or iii) Characterization of cell-penetrating peptides. Please, get in touch if interested.

[Mohammad ElGamacy @m_elgamacy]

@aracho133 @MPI_Bio This particular position has been filled already, but we shall announce new positions soon.

[Damietta Protein Design Toolkit @proteintoolkit]

The upgraded rotamer library (v1.60->v1.95):
- Glycine padding; Ac-GLY-X-GLY-NHMe instead of Ac-X-NHMe
- Higher temperature; 310 K instead of 293 K
- Simulated using CHARMM36 instead of CHARMM27

[Mohammad ElGamacy @m_elgamacy]

@Vikram_Alva @NAR_Open @DameLab @SammyBoterhammy @MPI_Bio @LeidenScience That was a lot of work! Congratulations to you all!

[Mohammad ElGamacy @m_elgamacy]

We just released the "protein design toolkit", integrating tools from Damietta, ProteinMPNN and OpenMM.

An interactive tutorial is available at the server https://t.co/gmoCK0BbfV. Recommended usage is described in the paper: https://t.co/Uxghy5MO1U and feedback is most welcome!

[Mohammad ElGamacy @m_elgamacy]

Our preprint on tuning of G-CSFR signalling. Many thanks to @PiehlerLab for the great collaboration!

https://t.co/qBBrqGZtHk

[Mohammad ElGamacy @m_elgamacy]

@ChrisWellsWood Getting more invasive lately

[Mohammad ElGamacy @m_elgamacy]

The link for the atlas: https://t.co/9Rq38HJADj

[Joana Pereira @Joana_MPereira]

So happy to see our work going live together with that of @pedrobeltrao and @thesteinegger today @nature! @biozentrum @UniBasel @ISBSIB @SWISS_MODEL
link: https://t.co/nyXCNgxAHg
link: https://t.co/X0j3HaC1Z6

[Mohammad ElGamacy @m_elgamacy]

Here is our new protein design engine. In short, it evaluates interaction energies through a single matrix operation!

We're happy to get your feedback on the early software (https://t.co/ddaOrhSU8h) or web-server (https://t.co/hwXm87GctW); high-performance releases to follow.

[Cell Reports Methods @CellRepMethods]

The design of functional proteins using tensorized energy calculations https://t.co/sakag4InQh