Protein Design
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Benchmarks
Most implemented
X-LoRA: Mixture of Low-Rank Adapter Experts, a Flexible Framework for Large Language Models with Applications in Protein Mechanics and Molecular Design
ProGen2: Exploring the Boundaries of Protein Language Models
RITA: a Study on Scaling Up Generative Protein Sequence Models
TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation
A Text-guided Protein Design Framework
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization
Papers
Generative modeling of intrinsically disordered protein regions by reinforcing sparse autoencoder features
Intrinsically disordered protein regions (IDRs) play central roles in cellular processes such as transcriptional regulation, signal transduction, and subcellular localization, yet their functional design remains challeng…
Protein Language ModelReinforcement LearningProtein DesignCODesign: Consistency from Data to Trajectory in All-Atom Protein Binder Co-Design
The central challenge in de novo protein design is generating plausible, mutually compatible structures and sequences, such that each designed sequence folds into its intended structure and the structure accommodates tha…
Protein DesignProtein Structure Prediction: From Evolutionary Constraints to Generative Modeling
Accurate protein structure prediction is fundamental to structural biology because protein structure underlies molecular function and provides a basis for mechanistic interpretation. Recent advances in deep learning have…
Protein Structure PredictionMultiple Sequence AlignmentProtein DesignChamaileon: Cross-Context Binder Design with Contextualized Modeling and Mixed Sampling
The rapid evolution of generative models has unlocked new potentials in protein binder design, a pivotal task in structural biology, by facilitating end-to-end generation via joint sequence-structure modeling or hallucin…
Protein DesignSciForge: An AI-Native, Multimodal Workbench for Scientific Discovery
Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve …
Protein DesignVariable-Length Generative Protein Design via Generalized Poisson Flow
The ability to generate variable-length proteins is crucial in protein design, where the optimal length is often unknown and tightly coupled to designability. Current diffusion- and flow-based generative models typically…
Protein Design