Pipeline and data for a structure-first census of the JAMM zinc isopeptidase site across 3,884 verified MPN-fold proteins. Catalytic-site positions are read by three-dimensional superposition onto a reference MPN+ domain (PDB 1R5X chain A) rather than by sequence alignment; fold membership is verified by secondary-stru...
Marc Zimmer· Zenodo (CERN European Organi...· 0 citations
Abstract: Classical AI answers from inside a representation fixed before the question arrives. What that representation can express, the system can answer; what lies outside it, no amount of parameters, data, search, or compute reaches. AlphaFold predicts through a learned representation; AlphaEvolve searches a space o...
Denise Holt, Denis Ovseyenko· Zenodo (CERN European Organi...· 0 citations
This dataset contains the complete computational records from seven 20-design pilot runs performed during the development and validation of BOLTRA v1.0.0 (BoltzGen Orchestration Layer for Targeted design and Results Analysis). BOLTRA is a guided and resumable workflow layer for BoltzGen that supports design-specificati...
Olanrewaju Ayodeji Durojaye, Soukayna Baammi, Mohamed Moussaoui et al.· Zenodo (CERN European Organi...· 0 citations
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and young adults. While low risk disease has a 90% survival probability, metastatic RMS has a dismal prognosis. Treatment options include chemotherapy and local therapy (surgery, radiotherapy) but suffer from serious long-term side effects. The...
C. Steinkühler, Mirko Brunetti, Cristina Maria Depalma et al.· Cancer Research· 0 citations
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Abstract Large language models and generative protein design promise to accelerate biotechnology, but it remains unclear whether they can engineer dynamic megasynth(et)ases whose activity depends on transient, context-specific domain interfaces. Non-ribosomal peptide synthetases (NRPSs) exemplify this challenge and pro...
Emre F. Bülbül, Seounggun Bang, Kevin George et al.· Nature Communications· 0 citations
A new development pathway for pediatric oncology is established in which successive therapeutics are generated using shared scientific, manufacturing, and translational infrastructure, thereby substantially reducing the incremental effort required to develop successive pediatric therapeutics.
U. Saini, Sougata Dey, Stephanie P. Vega et al.· Cancer Research· 0 citations
Initial public release of PepBench, a benchmark of de novo peptide-binder backbone templates for inverse-folding evaluation. Contents 353 two-chain peptide–receptor PDB complexes 12 protein targets Peptide backbone lengths of 8, 16, and 24 residues Chain A: backbone-only poly-glycine designed peptide Chain B: fixed rec...
ProteinQure (Canada), David Earl Hostallero, Glenn Butterfoss et al.· Zenodo (CERN European Organi...· 0 citations
Proteins carry out most biological functions, and their activities are governed by their higher-order structure (HOS), which arises from folding, assembly, and dynamic conformational rearrangements. These structures are not static but exist as ensembles of interconverting states that respond to environmental changes an...
Xinyi Kuang· Washington University in St....· 0 citations
Results show that, irrespective of the partner antibody, phosphorylated tau assays are more accurate than assays that also measure non-phosphorylated forms of the protein in differentiating Aβ + from Aβ − individuals, and indicate that BD-pTau217 may offer superior sensitivity for the early identification of AD patholo...
H. Gleerup, C. S. Musaeus, Cristiano Santos et al.· Molecular Neurodegeneration...· 0 citations
Identifying protein targets from phenotype-first or mechanism-uncertain compounds remains difficult because proteome-scale docking can generate thousands of structurally plausible interactions per compound. We developed a workflow that converts ranked proteome-scale docking profiles into stable Gene Ontology (GO) Biolo...
Chase M Harms, Judith Klein‐Seetharaman· bioRxiv (Cold Spring Harbor...· 0 citations
Introduction Choledocholithiasis or common bile duct stones (CBDS) is a frequent cause of hospitalization. Confirmed stones are usually removed by Endoscopic Retrograde Cholangiopancreatography (ERCP), but this procedure carries significant risks (infection, perforation, hemorrhage). Current guidelines from the Europea...
We present a theoretical and numerical study of protein folding kinetics and conformational transitions in complex free-energy landscapes using generalized Langevin equations with memory kernels and Fokker-Planck formalisms. Moving beyond standard deterministic approaches, we investigate non-equilibrium folding dynamic...
Henrietta Volkova· Zenodo (CERN European Organi...· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
