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This release contains the version of the FCKcat code associated with the manuscript: Overcoming systematic data biases enables accurate prediction of enzyme kcat fold-changes for computational protein design Authors: Yvan Rousset, Alexander Kroll, and Martin J. Lercher The data and trained model files required to repro...
Engineering extended macromolecular therapeutics requires comprehensive structural modeling to verify tertiary folding fidelity and domain accessibility across repetitive structural units. In this study, we present the structural characterization of KH-002v003, an ultra-large synthetic multivalent fusion protein constr...
PAK1 and PAK2 shielded RAS from LZTR1-dependent degradation by phosphorylating T148, and inhibiting PAK1/2 activity improved RAS-directed therapy, revealing a regulatory circuit governing RAS stability that is preferentially active in blood cancers and potentially druggable.
This Ada/SPARK program applies the V3 Architecture to the largest known protein — titin (connectin) — with 34,350 amino acids. The V3 model resolves the Levinthal paradox by replacing stochastic exploration with a deterministic phase transition guided by four invariants: Ψ_V3 = 48,016.8 kg·m⁻², Φ_critical = -51.1 mV, k...
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This Ada/SPARK program applies the V3 Architecture to the largest known protein — titin (connectin) — with 34,350 amino acids. The V3 model resolves the Levinthal paradox by replacing stochastic exploration with a deterministic phase transition guided by four invariants: Ψ_V3 = 48,016.8 kg·m⁻², Φ_critical = -51.1 mV, k...
# Cofolding benchmark: structures, alignments and analysis scripts Supplementary data for *Benchmarking Protein–Ligand Cofolding Models: Correct LigandPlacement Is Decoupled from Accurate Protein Conformation*. Seven protein–ligand complexes, three class A GPCRs and four kinase systems, were predictedwith AlphaFold3, B...
Protein structure modeling rests on a single computational primitive: the interaction between what a residue is (sequence content) and where it sits (three-dimensional geometry). What is the expressive limit of this layer class? We show that the complete bilinear operator over content-geometry outer products--the suffi...
This study investigated the effects of non-covalent modification of polysaccharides with different charge density on the emulsifying properties of myofibrillar proteins (MP). Carboxymethyl cellulose (CMC) with degree of substitution values of 0.7, 0.9, and 1.2 (correspond to low, medium, and high charge density) was se...
This work proposes a hardware platform based on small single-board computers that is extendable and scalable as well as easy to deploy, relying on an open design and illustrates how to build such a system without incurring high costs, high power consumption, or single points of failure.
This paper highlights the challenges to conduct proper affect-related studies with psychology, provides a comprehensive literature review in affect theory, and proposes guidelines for conducting psychoempirical software engineering.
The comparison of adopter and non-adopter sample reveals three potential adoption inhibitor, security, data privacy, and portability, which underlines the importance of the technical and security perspectives for research investigating the adoption of technology.
This study conducts a multiple case study on twenty European software startups and proposes a prototype-centric learning model in early stage software startups, and identifies factors that occur as barriers but also facilitators for prototyping in earlystage software startups.
Proof of concept for watermarking AI-generated proteins while preserving biological function.
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.
Scientists are using AlphaFold to strengthen a photosynthesis enzyme for resilient, heat-tolerant crops.
Explore how AlphaFold has accelerated science and fueled a global wave of biological discovery.
AlphaFold has revealed the structure of a key protein behind heart disease
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