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Leo Zang

@leozang.bsky.social
798 followers 22 following 54 posts

Protein Designer | Share Reading Notes (AI+Protein/RNA/DNA) www.leozang.com

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Leo Zang @leozang.bsky.social · 05/03/2025
Computational protein design - "This Primer provides an introduction to the main approaches in computational protein design, covering both physics-based and machine-learning-based tools. It aims to be accessible to biological, physical and computer scientists alike." www.nature.com/articles/s43...
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Leo Zang @leozang.bsky.social · 30/01/2025
We describe existing platforms for protein/peptide-based ligand identification and the drug delivery systems that might be exploited for the delivery of biologic-based degraders." Link: pubs.acs.org/doi/10.1021/...
pubs.acs.org
Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics
The nascent field of targeted protein degradation (TPD) could revolutionize biomedicine due to the ability of degrader molecules to selectively modulate disease-relevant proteins. A key limitation to ...
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Leo Zang @leozang.bsky.social · 30/01/2025
Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics - "we provide a comprehensive and critical review of studies that have used proteins and peptides to mediate the degradation and hence the functional control of otherwise challenging disease-relevant protein targets.
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Leo Zang @leozang.bsky.social · 23/01/2025
-- aim to approximate soft optimal denoising processes (a.k.a. policies in RL) that combine pre-trained denoising processes with value functions serving as look-ahead functions that predict from intermediate states to terminal rewards. "
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Leo Zang @leozang.bsky.social · 23/01/2025
- "We review these methods from a unified perspective, demonstrating that current techniques -- such as Sequential Monte Carlo (SMC)-based guidance, value-based sampling, and classifier guidance
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Leo Zang @leozang.bsky.social · 23/01/2025
Inference-Time Alignment in Diffusion Models with Reward-Guided Generation: Tutorial and Review arxiv.org/abs/2501.09685
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Leo Zang @leozang.bsky.social · 18/01/2025
- Construct full-length proteins with binding motifs and refining structures using the Rosetta FastDesign protocol and grafting (with a potential round of LigandMPNN optimization) - Engineer and validate binders for Bcl2–venetoclax, DB3–progesterone, and PDF1–actinonin through experimental testing
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Leo Zang @leozang.bsky.social · 18/01/2025
- Benchmark MaSIF-neosurf against RFAA on 14 ligand-induced PPI complexes with 8,907 decoys from PDBBind - Use MaSIF-search to predict buried surfaces and identify complementary surface fingerprints from a database of protein fragments (~640,000)
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Leo Zang @leozang.bsky.social · 18/01/2025
Targeting protein–ligand neosurfaces with a generalizable deep learning tool | @Nature - MaSIF-neosurf can design binders for protein-ligand complexes, targeting neosurfaces (i.e., ligand-induced structural changes on the protein surface) Link: www.nature.com/articles/s41...
nature.com
Targeting protein–ligand neosurfaces with a generalizable deep learning tool - Nature
A computational deep learning approach is used to design synthetic proteins that target the neosurfaces formed by protein–ligand interactions, with applications in the development of new therapeutic m...
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Leo Zang @leozang.bsky.social · 17/01/2025
- Train sequence based models to predict the activity of regulatory elements (MPRALegNet, MPRAnn, EnformerMPRA, and SeiMPRA) - Use MPRALegNet predicts TFBS combinations, fine-mapping and variant effects
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Leo Zang @leozang.bsky.social · 17/01/2025
Massively parallel characterization of transcriptional regulatory elements - Develope an optimized lentiMPRA (lentiviral massively parallel reporter assay) method to test regulatory activity of >680,000 sequences across three cell types (HepG2, K562, WTC11) Link: www.nature.com/articles/s41...
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Leo Zang @leozang.bsky.social · 09/01/2025
Integrating genetic algorithms and language models for enhanced enzyme design academic.oup.com/bib/article/...
academic.oup.com
Validate User
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Leo Zang @leozang.bsky.social · 09/01/2025
DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks www.biorxiv.org/content/10.1... Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data www.biorxiv.org/content/10.1...
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Leo Zang @leozang.bsky.social · 27/12/2024
- "This review systematically summarizes recent advances in chromatin interaction matrix prediction models...This article details various models, focusing on how one-dimensional (1D) information transforms into the 3D structure chromatin interactions"
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Leo Zang @leozang.bsky.social · 27/12/2024
A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles | @BriefingBioinfo Link: academic.oup.com/bib/article/...
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Leo Zang @leozang.bsky.social · 19/12/2024
EnzymeCAGE: A Geometric Foundation Model for Enzyme Retrieval with Evolutionary Insights www.biorxiv.org/content/10.1... Semantic mining of functional de novo genes from a genomic language model www.biorxiv.org/content/10.1...
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Leo Zang @leozang.bsky.social · 19/12/2024
Bridging Sequence-Structure Alignment in RNA Foundation Models arxiv.org/abs/2407.11242 Mapping targetable sites on the human surfaceome for the design of novel binders www.biorxiv.org/content/10.1...
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Leo Zang @leozang.bsky.social · 19/12/2024
NeuralPLexer3: Physio-Realistic Biomolecular Complex Structure Prediction with Flow Models arxiv.org/abs/2412.10743 FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction arxiv.org/abs/2412.10966
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Leo Zang @leozang.bsky.social · 19/12/2024
Leveraging ancestral sequence reconstruction for protein representation learning www.nature.com/articles/s42... Guiding Generative Protein Language Models with Reinforcement Learning arxiv.org/abs/2412.12979
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Leo Zang @leozang.bsky.social · 16/12/2024
Harnessing the biology of regulatory T cells to treat disease - "This Review will discuss recent advances in our understanding of human Treg cell biology, with a focus on mechanisms of action and strategies to assess outcomes of Treg cell-targeted therapies." www.nature.com/articles/s41...
nature.com
Harnessing the biology of regulatory T cells to treat disease - Nature Reviews Drug Discovery
Regulatory T cells keep the immune system in check to maintain homeostasis and restrain inflammation. This Review discusses strategies to harness these cells therapeutically for autoimmunity, transpla...
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Leo Zang @leozang.bsky.social · 16/12/2024
IgDesign: In vitro validated antibody design against multiple therapeutic antigens using inverse folding www.biorxiv.org/content/10.1...
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Leo Zang @leozang.bsky.social · 16/12/2024
Annotation-guided Protein Design with Multi-Level Domain Alignment arxiv.org/abs/2404.16866 BEACON: Benchmark for Comprehensive RNA Tasks and Language Models arxiv.org/abs/2406.10391
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Leo Zang @leozang.bsky.social · 15/12/2024
mRNA m6A detection | @MethodsPrimers - "This Primer outlines the available tools for detecting and mapping m6A, discusses the strengths and limitations of each method and offers guidance on selecting the most suitable approach." www.nature.com/articles/s43...
nature.com
mRNA m6A detection - Nature Reviews Methods Primers
N6-methyladenosine (m6A) is an mRNA modification influencing gene expression. Advanced methodologies for mapping m6A enhance understanding of its dynamic roles and interactions. In this Primer, Moshit...
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Leo Zang @leozang.bsky.social · 14/12/2024
- Use gradient-based approximation to modify protein sequences to increase/decrease specific concept values (e.g., which amino acids for increasing aromaticity).
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Leo Zang @leozang.bsky.social · 14/12/2024
- Train model with MLM Loss, Concept Loss (mean square error on concept embedding), and Orthogonality Loss (cosine similarity between known/unknown embeddings).
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Leo Zang @leozang.bsky.social · 14/12/2024
- Add Concept Bottleneck Module (using <cls> token) and Orthogonality Network to standard BERT-like architecture.
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Leo Zang @leozang.bsky.social · 14/12/2024
Concept Bottleneck Language Models For protein design - Introduce CB-pLM (Concept Bottleneck Protein Language Models) from 24M to 3B, trained on UniRef50 and SwissProt over 718 concepts (including Cluster name, Biological process, and Biopython-derived features, etc.) arxiv.org/abs/2411.06090
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Leo Zang @leozang.bsky.social · 12/12/2024
Benchmarking recent computational tools for DNA-binding protein identification - "we conduct an unbiased benchmarking of 11 state-of-the-art computational tools as well as traditional tools such as ScanProsite, BLAST, and HMMER for identifying DBPs." Link: academic.oup.com/bib/article/...
academic.oup.com
Benchmarking recent computational tools for DNA-binding protein identification
Abstract. Identification of DNA-binding proteins (DBPs) is a crucial task in genome annotation, as it aids in understanding gene regulation, DNA replicatio
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Leo Zang @leozang.bsky.social · 27/11/2024
Title correction: A general temperature-guided language model to design proteins of enhanced stability and activity
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Leo Zang @leozang.bsky.social · 27/11/2024
- Mouse level: Human-homologous protein data sourced from OGEE database - Cell line level: Protein essentiality data from Project Score database, providing insights across 323 different human cell lines
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Leo Zang @leozang.bsky.social · 27/11/2024
- Human level: Protein-coding genes from gnomAD database, annotated using LOEUF (Loss of Function Observed/Expected Upper Bound Fraction) metric (0.6 threshold) to classify essential vs non-essential proteins
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Leo Zang @leozang.bsky.social · 27/11/2024
Comprehensive prediction and analysis of human protein essentiality based on a pretrained large language model | @NatComputSci - PIC (Protein Importance Calculator), an ESM2-based deep learning model, predicts protein essentiality across three biological levels Link: www.nature.com/articles/s43...
nature.com
Comprehensive prediction and analysis of human protein essentiality based on a pretrained large language model - Nature Computational Science
This study introduces the Protein Importance Calculator (PIC), a deep learning model designed to predict human essential proteins (HEPs) crucial for survival and development. Unlike conventional metho...
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Leo Zang @leozang.bsky.social · 27/11/2024
[1] link.springer.com/article/10.1...
link.springer.com
Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures - BMC Microbiology
Background The ambient temperature of all habitats is a key physical property that shapes the biology of microbes inhabiting them. The optimal growth temperature (OGT) of a microbe, is therefore a key...
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Leo Zang @leozang.bsky.social · 27/11/2024
Using artificial intelligence to document the hidden RNA virosphere - PRIME, protein language model (same as ESM-2 650M architecture) pretrained on 96 million sequences with optimal growth temperatures (OGTs annotated by [1]) with MLM, MSE, and Correlation Loss Link: www.science.org/doi/10.1126/...
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Leo Zang @leozang.bsky.social · 27/11/2024
Getting aligned on representational alignment - "In this Perspective, we survey the exciting recent developments in representational alignment research in the fields of cognitive science, neuroscience, and machine learning" Link: arxiv.org/abs/2310.13018
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Leo Zang @leozang.bsky.social · 25/11/2024
- miRTarBase 2025: updates to the collection of experimentally validated microRNA–target interactions academic.oup.com/nar/advance-... - miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification academic.oup.com/nar/advance-...
academic.oup.com
miRTarBase 2025: updates to the collection of experimentally validated microRNA–target interactions
Abstract. MicroRNAs (miRNAs) are small non-coding RNAs (18–26 nucleotides) that regulate gene expression by interacting with target mRNAs, affecting variou
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Leo Zang @leozang.bsky.social · 25/11/2024
More: - BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data academic.oup.com/nar/advance-... - BFVD—a large repository of predicted viral protein structures academic.oup.com/nar/advance-...
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Reposted by Leo Zang
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 23/11/2024
Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. 🌐 bfvd.foldseek.com 💾 bfvd.steineggerlab.workers.dev 📄 academic.oup.com/nar/advance-...
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Leo Zang @leozang.bsky.social · 21/11/2024
- InterPro: the protein sequence classification resource in 2025 academic.oup.com/nar/advance-...
academic.oup.com
InterPro: the protein sequence classification resource in 2025
Abstract. InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrate
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Leo Zang @leozang.bsky.social · 21/11/2024
Now, combining the resulting catalogs of interactions with complementary methods, including crosslinking MS (XL-MS) and cryogenic electron microscopy (cryo-EM), helps distinguish direct interactions from indirect ones within the same or between different protein complexes."
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Leo Zang @leozang.bsky.social · 21/11/2024
- "As new technologies emerged, analysis of PPIs increased to a genome-wide scale with the introduction of intracellular tagging methods, affinity purification (AP) followed by mass spectrometry (MS), and co-fractionation MS (CF-MS).
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Leo Zang @leozang.bsky.social · 21/11/2024
Discovery and significance of protein-protein interactions in health and disease | @cellpressnews.bsky.social Review Link: www.cell.com/cell/fulltex...
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Leo Zang @leozang.bsky.social · 21/11/2024
- CATH v4.4: major expansion of CATH by experimental and predicted structural data academic.oup.com/nar/advance-...
academic.oup.com
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Leo Zang @leozang.bsky.social · 21/11/2024
Database updates -The Pfam protein families database: embracing AI/ML academic.oup.com/nar/advance-... - UniProt: the Universal Protein Knowledgebase in 2025 academic.oup.com/nar/advance-... - RASP v2.0: an updated atlas for RNA structure probing data academic.oup.com/nar/advance-...
academic.oup.com
UniProt: the Universal Protein Knowledgebase in 2025
Abstract. The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely acce
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Leo Zang @leozang.bsky.social · 19/11/2024
@bsky.app Can you increase the character limit for threads?
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Leo Zang @leozang.bsky.social · 19/11/2024
- Control model predictions through feature steering and use Claude-3.5 Sonnet to automatically interpret features using protein metadata
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Leo Zang @leozang.bsky.social · 19/11/2024
- Train 20 SAEs per layer with 32x expansion factor (expanding from 320 to 10,240 features) on 5M randomly selected proteins from UniRef50 - Identify up to 2,548 interpretable latent features per layer that correlate with up to 143 known biological concepts
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Leo Zang @leozang.bsky.social · 19/11/2024
InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders www.biorxiv.org/content/10.1... - Use sparse autoencoders (SAEs) to extract and analyze interpretable features from ESM-2-8M
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Leo Zang @leozang.bsky.social · 17/11/2024
jclinic.mit.edu/boltz-1/
jclinic.mit.edu
Introducing Boltz-1: Democratizing Biomolecular Interaction Modeling – MIT Jameel Clinic
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Leo Zang @leozang.bsky.social · 16/11/2024
miRBench: A Comprehensive microRNA Binding Site Prediction Training and Benchmarking Dataset Preprint: www.biorxiv.org/content/10.1... GitHub: github.com/katarinagres...
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