Moritz Ertelt
@moritzertelt.bsky.social
Biologist designing proteins
Postdoc at Fraunhofer IIP in Munich/Penzberg
https://moritzertelt.github.io/
Postdoc at Fraunhofer IIP in Munich/Penzberg
https://moritzertelt.github.io/
Today is the last day of the Ginkgo antibody developability challenge, curious to see whether someone came up with a deep learning approach that actually out competes the biophysical baselines
github.com/ginkgobiowor...
github.com/ginkgobiowor...
November 17, 2025 at 6:32 AM
Today is the last day of the Ginkgo antibody developability challenge, curious to see whether someone came up with a deep learning approach that actually out competes the biophysical baselines
github.com/ginkgobiowor...
github.com/ginkgobiowor...
Reposted by Moritz Ertelt
De novo design of phospho-tyrosine peptide binders [new]
Designs binders for phosphorylated tyrosine sites on clinically relevant targets using a deep generative framework, enabling modulation of signaling pathways.
Designs binders for phosphorylated tyrosine sites on clinically relevant targets using a deep generative framework, enabling modulation of signaling pathways.
September 30, 2025 at 9:12 PM
De novo design of phospho-tyrosine peptide binders [new]
Designs binders for phosphorylated tyrosine sites on clinically relevant targets using a deep generative framework, enabling modulation of signaling pathways.
Designs binders for phosphorylated tyrosine sites on clinically relevant targets using a deep generative framework, enabling modulation of signaling pathways.
Super excited for the full data, especially to see which of the over 400 screened binders actually got us the third place 🥳
Shout-out to the organizers for this very cool competition!
Shout-out to the organizers for this very cool competition!
🚨The Bits to Binders Competition has concluded!🧬
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
September 2, 2025 at 6:10 PM
Super excited for the full data, especially to see which of the over 400 screened binders actually got us the third place 🥳
Shout-out to the organizers for this very cool competition!
Shout-out to the organizers for this very cool competition!
NaturalAntibody+BI benchmarking IF models on internal antibody data:
"... IF models are moderately useful in an industrial setting for filtering NGS datasets."
Also from their data antibody-specific models seem to be better than their base models and antigens don't substantially alter predictions
"... IF models are moderately useful in an industrial setting for filtering NGS datasets."
Also from their data antibody-specific models seem to be better than their base models and antigens don't substantially alter predictions
Benchmarking antigen-aware inverse folding methods for antibody design. https://www.biorxiv.org/content/10.1101/2025.08.05.668698v1
August 8, 2025 at 9:36 AM
NaturalAntibody+BI benchmarking IF models on internal antibody data:
"... IF models are moderately useful in an industrial setting for filtering NGS datasets."
Also from their data antibody-specific models seem to be better than their base models and antigens don't substantially alter predictions
"... IF models are moderately useful in an industrial setting for filtering NGS datasets."
Also from their data antibody-specific models seem to be better than their base models and antigens don't substantially alter predictions
Really cool to see this out!
As someone with a more structural background looking for a phage genome annotation tool this was more than I'd ever hoped for 😄
As someone with a more structural background looking for a phage genome annotation tool this was more than I'd ever hoped for 😄
Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1
August 7, 2025 at 10:31 AM
Really cool to see this out!
As someone with a more structural background looking for a phage genome annotation tool this was more than I'd ever hoped for 😄
As someone with a more structural background looking for a phage genome annotation tool this was more than I'd ever hoped for 😄
Reposted by Moritz Ertelt
In 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known.
Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.
Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.
July 25, 2025 at 10:05 PM
In 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known.
Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.
Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.
Reposted by Moritz Ertelt
We have a new preprint out on the Masala software suite, a free and open-source platform for easy biomolecular modelling methods development. www.biorxiv.org/content/10.1...
The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design
Although canonical protein design has benefited from machine learning methods trained on databases of protein sequences and structures, synthetic heteropolymer design still relies heavily on physics-b...
www.biorxiv.org
July 14, 2025 at 1:07 PM
We have a new preprint out on the Masala software suite, a free and open-source platform for easy biomolecular modelling methods development. www.biorxiv.org/content/10.1...
Reposted by Moritz Ertelt
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
Reposted by Moritz Ertelt
Register for SRC25 Workshop (tinyurl.com/SRC25-worksh...) : How to train your model - This immersive, hands-on advanced-level event is designed for researchers who are ready to move beyond “out-of-the-box” machine learning models for protein design.
How to train your model
Event dates Sunday 8/3 1pm - 10pm Monday 8/4 7am - 2pm Friday 8/8 9am-10pm Saturday 8/9 Travel Application Link This immersive, hands-on event is designed for researchers who are ready to move beyo...
tinyurl.com
May 21, 2025 at 7:35 PM
Register for SRC25 Workshop (tinyurl.com/SRC25-worksh...) : How to train your model - This immersive, hands-on advanced-level event is designed for researchers who are ready to move beyond “out-of-the-box” machine learning models for protein design.
Reposted by Moritz Ertelt
One-day novice-level course surveying popular tools and workflow for modern protein design with brief exploration of common applications including antibody design and binder design: 1-day Protein Design Workshop. Register here: tinyurl.com/SRC25-worksh...
1-day Protein Design Workshop @ SRC 2025
AI-Driven Design of Biologics: Hands-on Guide to Using State-of-the-Art ML Protein Models brought to you by the Rosetta Commons Event dates Sunday 8/3 1pm - 6 pm Monday 8/4 8am - 2 pm Event Locati...
tinyurl.com
May 21, 2025 at 7:37 PM
One-day novice-level course surveying popular tools and workflow for modern protein design with brief exploration of common applications including antibody design and binder design: 1-day Protein Design Workshop. Register here: tinyurl.com/SRC25-worksh...
Reposted by Moritz Ertelt
Thrilled to announce that this year’s European RosettaCon protein design conference will take place in Ljubljana, Oct 20–22, 2025!
Open to all, with a remote keynote by Nobel laureate David Baker.
More info coming soon — it’s going to be amazing! Hope to see you there!
Open to all, with a remote keynote by Nobel laureate David Baker.
More info coming soon — it’s going to be amazing! Hope to see you there!
March 17, 2025 at 12:06 PM
Thrilled to announce that this year’s European RosettaCon protein design conference will take place in Ljubljana, Oct 20–22, 2025!
Open to all, with a remote keynote by Nobel laureate David Baker.
More info coming soon — it’s going to be amazing! Hope to see you there!
Open to all, with a remote keynote by Nobel laureate David Baker.
More info coming soon — it’s going to be amazing! Hope to see you there!
Reposted by Moritz Ertelt
The Praetorius lab for Biomolecular Design at the Institute of Science and Technology Austria (ISTA) is looking for grad students in 2024. If you are interested in protein design at a great institute near Vienna reach out to me!
www.dropbox.com/scl/fi/6iny2...
www.dropbox.com/scl/fi/6iny2...
www.dropbox.com
November 28, 2023 at 1:08 AM
The Praetorius lab for Biomolecular Design at the Institute of Science and Technology Austria (ISTA) is looking for grad students in 2024. If you are interested in protein design at a great institute near Vienna reach out to me!
www.dropbox.com/scl/fi/6iny2...
www.dropbox.com/scl/fi/6iny2...