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Protein Design

Papers archive 2025-07-28

archive papers tagged: 175 · with a code link: 74 · where Syntology ran a sample: 31 (24 with a run with no instrument failure, 7 where every run was a failure of Syntology's instrument) Syntology

Show: all tagged papersonly where code ran (31 of 175 tagged: 24 with a run with no instrument failure, 7 where every run was a failure of Syntology's instrument)

Page 2 of 2: papers 101 to 175 of 175, in archive order: by repositories listed in the archive (most first), then newest first, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers that list no repository come after every paper that lists one.

Papers without a page here are shown as plain text. A Syntology line reads “N ran (of which C constructed an object rather than computing a result; K with no instrument failure: H honoured, V violated, P with no contract checked; I where Syntology's instrument failed) · U unverified”; the figure “where Syntology's instrument failed” counts failures of Syntology's instrument, not of the code. When the archive marks a repository official for the paper, the line starts with that repository's state (the archive's flag, not a verdict on who wrote the code); hover it for the repositories the samples that ran came from. Abstracts are on each paper's page.

• Inference-Time Alignment in Diffusion Models with Reward-Guided Generation: Tutorial and Review
  16 Jan 2025 0 repositories listed
• From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering
  5 Jan 2025 0 repositories listed
• A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design
  2 Jan 2025 0 repositories listed
• Multi-Attribute Constraint Satisfaction via Language Model Rewriting
  26 Dec 2024 0 repositories listed
• Open-Source Protein Language Models for Function Prediction and Protein Design
  18 Dec 2024 0 repositories listed
• ProtDAT: A Unified Framework for Protein Sequence Design from Any Protein Text Description
  5 Dec 2024 0 repositories listed
• MADE: Graph Backdoor Defense with Masked Unlearning
  26 Nov 2024 0 repositories listed
• Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design
  26 Nov 2024 0 repositories listed
• Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab
  9 Nov 2024 0 repositories listed
• ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design
  8 Nov 2024 0 repositories listed
• EMOCPD: Efficient Attention-based Models for Computational Protein Design Using Amino Acid Microenvironment
  28 Oct 2024 0 repositories listed
• Training Free Guided Flow Matching with Optimal Control
  23 Oct 2024 0 repositories listed
• MeMDLM: De Novo Membrane Protein Design with Masked Discrete Diffusion Protein Language Models
  22 Oct 2024 0 repositories listed
• What Do LLMs Need to Understand Graphs: A Survey of Parametric Representation of Graphs
  16 Oct 2024 0 repositories listed
• Computational design of target-specific linear peptide binders with TransformerBeta
  7 Oct 2024 0 repositories listed
• Plug-and-Play Controllable Generation for Discrete Masked Models
  3 Oct 2024 0 repositories listed
• Towards deep learning sequence-structure co-generation for protein design
  2 Oct 2024 0 repositories listed
• Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design
  27 Sep 2024 0 repositories listed
• Recent advances in interpretable machine learning using structure-based protein representations
  26 Sep 2024 0 repositories listed
• De novo design of high-affinity protein binders with AlphaProteo
  12 Sep 2024 0 repositories listed
• ProteinBench: A Holistic Evaluation of Protein Foundation Models
  10 Sep 2024 0 repositories listed
• Leveraging Deep Generative Model For Computational Protein Design And Optimization
  30 Aug 2024 0 repositories listed
• BERT and LLMs-Based avGFP Brightness Prediction and Mutation Design
  30 Jul 2024 0 repositories listed
• RNACG: A Universal RNA Sequence Conditional Generation model based on Flow-Matching
  29 Jul 2024 0 repositories listed
• Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design
  15 Jul 2024 0 repositories listed
• Reinforcement Learning for Sequence Design Leveraging Protein Language Models
  3 Jul 2024 0 repositories listed
• Fast uncovering of protein sequence diversity from structure
  17 Jun 2024 0 repositories listed
• UniIF: Unified Molecule Inverse Folding
  29 May 2024 0 repositories listed
• Implicitly Guided Design with PropEn: Match your Data to Follow the Gradient
  28 May 2024 0 repositories listed
• SurfPro: Functional Protein Design Based on Continuous Surface
  7 May 2024 0 repositories listed
• Model-based reinforcement learning for protein backbone design
  3 May 2024 0 repositories listed
• ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering
  21 Apr 2024 0 repositories listed
• Annotation-guided Protein Design with Multi-Level Domain Alignment
  18 Apr 2024 0 repositories listed
• Using GANs for De Novo Protein Design Targeting Microglial IL-3Rα to Inhibit Alzheimer's Progression
  5 Apr 2024 0 repositories listed
• Diffusion on language model encodings for protein sequence generation
  6 Mar 2024 0 repositories listed
• Generative AI for Controllable Protein Sequence Design: A Survey
  16 Feb 2024 0 repositories listed
• Learning immune receptor representations with protein language models
  6 Feb 2024 0 repositories listed
• Enhancing the efficiency of protein language models with minimal wet-lab data through few-shot learning
  3 Feb 2024 0 repositories listed
• A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
  14 Dec 2023 0 repositories listed
• AI-predicted protein deformation encodes energy landscape
  30 Nov 2023 0 repositories listed
• Generative artificial intelligence for de novo protein design
  15 Oct 2023 0 repositories listed
• DockGame: Cooperative Games for Multimeric Rigid Protein Docking
  9 Oct 2023 0 repositories listed
• Backdiff: a diffusion model for generalized transferable protein backmapping
  3 Oct 2023 0 repositories listed
• Boosting AND/OR-Based Computational Protein Design: Dynamic Heuristics and Generalizable UFO
  31 Aug 2023 0 repositories listed
• Metropolis Sampling for Constrained Diffusion Models
  11 Jul 2023 0 repositories listed Syntology 8 ran (of which 0 constructed an object rather than computing a result; 8 with no instrument failure: 0 honoured, 0 violated, 8 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified (of 8 harvested samples)
• Gradient-Informed Quality Diversity for the Illumination of Discrete Spaces
  8 Jun 2023 0 repositories listed
• CCPL: Cross-modal Contrastive Protein Learning
  19 Mar 2023 0 repositories listed
• Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action
  13 Feb 2023 0 repositories listed
• Protein Structure Prediction until CASP15
  15 Dec 2022 0 repositories listed
• TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs
  27 Apr 2022 0 repositories listed
• Controllable Protein Design with Language Models
  18 Jan 2022 0 repositories listed
• Benchmarking deep generative models for diverse antibody sequence design
  12 Nov 2021 0 repositories listed
• Design in the Dark: Learning Deep Generative Models for De Novo Protein Design
  29 Sep 2021 0 repositories listed
• Fast fixed-backbone protein sequence and rotamer design
  29 Sep 2021 0 repositories listed
• PDBench: Evaluating Computational Methods for Protein Sequence Design
  16 Sep 2021 0 repositories listed
• Deep Generative Modeling for Protein Design
  31 Aug 2021 0 repositories listed
• Efficient generative modeling of protein sequences using simple autoregressive models
  4 Mar 2021 0 repositories listed
• Mimetic Neural Networks: A unified framework for Protein Design and Folding
  7 Feb 2021 0 repositories listed
• Conditional Generative Modeling for De Novo Hierarchical Multi-Label Functional Protein Design
  1 Jan 2021 0 repositories listed
• Designing a Prospective COVID-19 Therapeutic with Reinforcement Learning
  3 Dec 2020 0 repositories listed
• Pre-training of Graph Neural Network for Modeling Effects of Mutations on Protein-Protein Binding Affinity
  28 Aug 2020 0 repositories listed
• Lattice protein design using Bayesian learning
  14 Mar 2020 0 repositories listed
• Generative modeling for protein structures
  1 Dec 2018 0 repositories listed
• Void distributions reveal structural link between jammed packings and protein cores
  31 Oct 2018 0 repositories listed
• A natural upper bound to the accuracy of predicting protein stability changes upon mutations
  27 Sep 2018 0 repositories listed
• Modular decomposition of protein structure using community detection
  18 Sep 2018 0 repositories listed
• Computational Protein Design with Deep Learning Neural Networks
  24 Feb 2018 0 repositories listed
• Prediction of amino acid side chain conformation using a deep neural network
  26 Jul 2017 0 repositories listed
• Protein design by multiobjective optimization: evolutionary and non-evolutionary approaches
  1 Jul 2017 0 repositories listed
• Rigidity strengthening is a vital mechanism for protein-ligand binding
  31 Mar 2017 0 repositories listed
• Folding and Stabilization of Native-Sequence-Reversed Proteins
  16 Jun 2016 0 repositories listed
• Ideal gas behavior of rotamerically defined conformers in native globular proteins
  30 Apr 2015 0 repositories listed
• Computational Protein Design Using AND/OR Branch-and-Bound Search
  8 Dec 2014 0 repositories listed
• MAP Estimation for Graphical Models by Likelihood Maximization
  1 Dec 2010 0 repositories listed
• Clusters and Coarse Partitions in LP Relaxations
  1 Dec 2008 0 repositories listed

Syntology lines on 1 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; each line links to that paper's sample list. Syntology's record for this page has not changed since 2026-09-28, the first build that kept a record date for it; when this build read Syntology's graph is in the build record. For agents: get_harvested_code_for_paper(arxiv_id) lists each paper's samples; how to connect.