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Showing 1 to 6 of 6 for “"RFdiffusion"”.
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Generative Diffusion Models Towards De Novo Protein Design
… biologists to develop RoseTTAFold Diffusion (RFdiffusion). By combining the structure prediction capabilities of RoseTTAFold and diffusion modeling principles, RFdiffusion can generate functional proteins with in vitro validated properties such as high-affinity binders and symmetric protein …
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Computational design of functional cyclic peptides using deep learning
… cyclic offset to the AlphaFold2 network as well RFdiffusion, resulting in accurate prediction and design of structured de novo cyclic peptides and high affinity cyclic peptide binders against protein targets of interest of diverse shape and function.
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Integrin-independent activation of Tie2 using the de novo designed protein H8mb
… protein that overcomes these constraints. We use RFdiffusion to design a stable, high-affinity Tie2 binder that functions as a selective antagonist when monomeric, but as a potent agonist when octavalent (H8mb) that activates the Tie2/pAKT pathway without binding to α5β1 integrin. H8mb induces …
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Casting Protein Structure Predictors as Energy-Based Models for Binder Design and Scoring
… in silico success rates compared to BindCraft, RFDiffusion, and ESM3. Beyond design, we evaluate pTMEnergy as an unsupervised scoring function for retrospective virtual screening tasks. Without any task-specific supervision or retraining, pTMEnergy consistently outperforms baseline methods …
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De novo Design of Mini-Protein Binders Targeting Allosteric Sites of MALT1 Towards Cancer Therapeutics
… de novo δημιουργία πρωτεϊνικών σκελετών με RFdiffusion (100.000 ανά θέση), σχεδιασμό αμινοξικής αλληλουχίας με SolubleMPNN, δομικό έλεγχο με AlphaFold3 όλων των συμπλόκων προσδέτη-MALT1, σειριακό φιλτράρισμα δύο σταδίων με κριτήρια δομικής αξιοπιστίας και δυνατότητας ανάπτυξης στο …
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Rational Identification of Neuropilin-1 Inhibitors: From Deep-Learning to Drug Repurposing
… that were generated by state-of-the-art tool, RFdiffusion. The peptides were designed to fit the NRP1-b1 pocket and engage hotspot residues identified by the canonical interaction between NRP1 and VEGF-A165. Their binding poses and apparent affinities were assessed, together with inhibitory …