Protein Design

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

2 leaderboard tables shown for this task, 2 with rows (a “benchmark” on this site is a table with at least one row, as on /sota), ordered by row count. “Best model” is the first row in the archive's own order at snapshot; nothing is re-ranked here and metric direction is not recorded in the archive. PwC's Trend sparklines are not in the archive, so that column is omitted.

Syntology column: samples harvested from the paper's repositories and executed on synthesized fixtures; “ran” is not a correctness claim and does not order the table. A dash means no Syntology record for that paper, not a recorded non-run. Read from the graph 2026-09-24.

Libraries

Not in the archive: the export carries no per-task library table, so there is nothing to show at snapshot 2025-07-28.

Datasets archive 2025-07-28

6 datasets whose archive record lists this task, ordered by the archive's paper count.

Subtasks archive 2025-07-28

No subtask under this task in the archive's task tree.

Most implemented papers archive 2025-07-28

30 shown of 74 papers with code (175 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• X-LoRA: Mixture of Low-Rank Adapter Experts, a Flexible Framework for Large Language Models with Applications in Protein Mechanics and Molecular Design
  11 Feb 2024 4 repositories listed
  Starting with a set of pre-trained LoRA adapters, our gating strategy uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create…
• ProGen2: Exploring the Boundaries of Protein Language Models
  27 Jun 2022 4 repositories listed Syntology ran 8 of 18 samples · 10 unverified · 2 pointer-only (licence)
  Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design.
• RITA: a Study on Scaling Up Generative Protein Sequence Models
  11 May 2022 4 repositories listed Syntology ran 1 of 2 samples · 1 unverified
  In this work we introduce RITA: a suite of autoregressive generative models for protein sequences, with up to 1.
• TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation
  27 Feb 2024 3 repositories listed
  In this work, we propose TaxDiff, a taxonomic-guided diffusion model for controllable protein sequence generation that combines biological species information with the generative capabilities of diffusion models to…
• A Text-guided Protein Design Framework
  9 Feb 2023 3 repositories listed Syntology ran 2 of 3 samples · 1 unverified · 1 pointer-only (licence)
  Current AI-assisted protein design mainly utilizes protein sequential and structural information.
• Geometry-Complete Diffusion for 3D Molecule Generation and Optimization
  8 Feb 2023 3 repositories listed Syntology ran 3 of 10 samples · 7 unverified
  Importantly, we demonstrate that the geometry-complete denoising process of GCDM learned for 3D molecule generation enables the model to generate a significant proportion of valid and energetically-stable large…
• Learning from Protein Structure with Geometric Vector Perceptrons
  3 Sep 2020 3 repositories listed Syntology ran 5 of 6 samples · 1 unverified · 6 pointer-only (licence)
  Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and…
• Improved motif-scaffolding with SE(3) flow matching
  8 Jan 2024 2 repositories listed Syntology ran 7 of 9 samples · 2 unverified
  Protein design often begins with the knowledge of a desired function from a motif which motif-scaffolding aims to construct a functional protein around.
• Fast protein backbone generation with SE(3) flow matching
  8 Oct 2023 2 repositories listed
  We present FrameFlow, a method for fast protein backbone generation using SE(3) flow matching.
• Practical and Asymptotically Exact Conditional Sampling in Diffusion Models
  30 Jun 2023 2 repositories listed Syntology ran 9 of 15 samples · 6 unverified · 15 pointer-only (licence)
  Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation.
• Unsupervisedly Prompting AlphaFold2 for Few-Shot Learning of Accurate Folding Landscape and Protein Structure Prediction
  20 Aug 2022 2 repositories listed Syntology ran 2 of 12 samples · 10 unverified · 2 pointer-only (licence)
  Data-driven predictive methods which can efficiently and accurately transform protein sequences into biologically active structures are highly valuable for scientific research and medical development.
• Variational auto-encoding of protein sequences
  9 Dec 2017 2 repositories listed
  Here we present an embedding of natural protein sequences using a Variational Auto-Encoder and use it to predict how mutations affect protein function.
• Improving large language models with concept-aware fine-tuning
  9 Jun 2025 1 repository listed
  Large language models (LLMs) have become the cornerstone of modern AI.
• Diffusion Sequence Models for Enhanced Protein Representation and Generation
  9 Jun 2025 1 repository listed
  We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences.
• CFP-Gen: Combinatorial Functional Protein Generation via Diffusion Language Models
  28 May 2025 1 repository listed
  Existing PLMs generate protein sequences based on a single-condition constraint from a specific modality, struggling to simultaneously satisfy multiple constraints across different modalities.
• PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models
  13 May 2025 1 repository listed
  While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and…
• Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation
  2 May 2025 1 repository listed Syntology ran 0 of 3 samples · 3 unverified
  Advances in protein engineering have the potential to revolutionize biotechnology and healthcare by designing proteins with tailored properties.
• Multi-Objective Quality-Diversity in Unstructured and Unbounded Spaces
  28 Mar 2025 1 repository listed
  However, existing methods in MOQD rely on tessellating the feature space into a grid structure, which prevents their application in domains where feature spaces are unknown or must be learned, such as complex biological…
• Proteina: Scaling Flow-based Protein Structure Generative Models
  2 Mar 2025 1 repository listed Syntology ran 1 of 1 samples · 0 unverified · 1 pointer-only (licence)
  Here, we develop Proteina, a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture with up to 5x…
• ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation
  20 Feb 2025 1 repository listed
  Protein backbone generation plays a central role in de novo protein design and is significant for many biological and medical applications.
• MotifBench: A standardized protein design benchmark for motif-scaffolding problems
  18 Feb 2025 1 repository listed
  The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse…
• Persistent Sheaf Laplacian Analysis of Protein Flexibility
  12 Feb 2025 1 repository listed
  Protein flexibility, measured by the B-factor or Debye-Waller factor, is essential for protein functions such as structural support, enzyme activity, cellular communication, and molecular transport.
• Controllable Protein Sequence Generation with LLM Preference Optimization
  25 Jan 2025 1 repository listed
  Designing proteins with specific attributes offers an important solution to address biomedical challenges.
• A General Framework for Inference-time Scaling and Steering of Diffusion Models
  12 Jan 2025 1 repository listed Syntology ran 1 of 1 samples · 0 unverified · 1 pointer-only (licence)
  For steering text-to-image models with a human preference reward, we find that FK steering a 0.
• Building Confidence in Deep Generative Protein Design
  27 Nov 2024 1 repository listed Syntology ran 0 of 5 samples · 5 unverified
  Deep generative models show promise for de novo protein design, but their effectiveness within specific protein families remains underexplored.
• Beyond Human-Like Processing: Large Language Models Perform Equivalently on Forward and Backward Scientific Text
  17 Nov 2024 1 repository listed
  The impressive performance of large language models (LLMs) has led to their consideration as models of human language processing.
• Concept Bottleneck Language Models For protein design
  9 Nov 2024 1 repository listed Syntology ran 0 of 1 samples · 1 unverified
  We introduce Concept Bottleneck Protein Language Models (CB-pLM), a generative masked language model with a layer where each neuron corresponds to an interpretable concept.
• Bridge-IF: Learning Inverse Protein Folding with Markov Bridges
  4 Nov 2024 1 repository listed Syntology ran 0 of 3 samples · 3 unverified
  To fill these gaps, we propose Bridge-IF, a generative diffusion bridge model for inverse folding, which is designed to learn the probabilistic dependency between the distributions of backbone structures and protein…
• Peptide-GPT: Generative Design of Peptides using Generative Pre-trained Transformers and Bio-informatic Supervision
  25 Oct 2024 1 repository listed
  In this work, we introduce PeptideGPT, a protein language model tailored to generate protein sequences with distinct properties: hemolytic activity, solubility, and non-fouling characteristics.
• Reinforcement learning on structure-conditioned categorical diffusion for protein inverse folding
  22 Oct 2024 1 repository listed
  To address this, we present RL-DIF, a categorical diffusion model for inverse folding that is pre-trained on sequence recovery and tuned via reinforcement learning on structural consistency.

Syntology lines on 14 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.