Protein Folding

Benchmarks archive 2025-07-28

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Libraries

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Datasets archive 2025-07-28

1 dataset whose archive record lists this task, ordered by the archive's paper count.

Subtasks archive 2025-07-28

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Most implemented papers archive 2025-07-28

30 shown of 51 papers with code (185 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.

• Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges
  27 Apr 2021 6 repositories listed
  The last decade has witnessed an experimental revolution in data science and machine learning, epitomised by deep learning methods.
• Highly accurate protein structure prediction with AlphaFold
  15 Jul 2021 5 repositories listed
  Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics.
• Rethinking Neural Operations for Diverse Tasks
  29 Mar 2021 3 repositories listed Syntology ran 18 of 34 samples · 16 unverified
  An important goal of AutoML is to automate-away the design of neural networks on new tasks in under-explored domains.
• Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation
  2 Jun 2023 2 repositories listed
  The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision.
• State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
  30 Sep 2022 2 repositories listed
  The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life.
• ParaFold: Paralleling AlphaFold for Large-Scale Predictions
  11 Nov 2021 2 repositories listed
  We evaluated the accuracy and efficiency of optimizations on CPUs and GPUs, and showed the large-scale prediction capability by running ParaFold inferences of 19, 704 small proteins in five hours on one NVIDIA DGX-2.
• TorchMD: A deep learning framework for molecular simulations
  22 Dec 2020 2 repositories listed
  Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials.
• Variational Encoding of Complex Dynamics
  23 Nov 2017 2 repositories listed Syntology ran 1 of 1 samples · 0 unverified
  Recent work in the field of deep learning has led to the development of variational autoencoders (VAE), which are able to compress complex datasets into simpler manifolds.
• MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models
  24 Jun 2025 1 repository listed
  Protein structure prediction models such as AlphaFold3 (AF3) push the frontier of biomolecular modeling by incorporating science-informed architectural changes to the transformer architecture.
• Probably Approximately Correct Labels
  12 Jun 2025 1 repository listed Syntology ran 1 of 4 samples · 3 unverified · 4 pointer-only (licence)
  Obtaining high-quality labeled datasets is often costly, requiring either extensive human annotation or expensive experiments.
• 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.
• PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL
  1 Feb 2025 1 repository listed
  PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system.
• Mask prior-guided denoising diffusion improves inverse protein folding
  10 Dec 2024 1 repository listed
  Inverse protein folding generates valid amino acid sequences that can fold into a desired protein structure, with recent deep-learning advances showing significant potential and competitive performance.
• 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…
• Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling
  10 Oct 2024 1 repository listed Syntology ran 12 of 13 samples · 1 unverified
  Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational challenges due to an exponentially large space of trajectories.
• TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering
  27 Aug 2024 1 repository listed
  While large language models (LLMs) have achieved much progress in the domain of natural language processing, their potential in protein engineering remains largely unexplored.
• Clustering for Protein Representation Learning
  30 Mar 2024 1 repository listed
  We select the highest-scoring clusters and use their medoid nodes for the next iteration of clustering, until we obtain a hierarchical and informative representation of the protein.
• Learning Collective Variables with Synthetic Data Augmentation through Physics-Inspired Geodesic Interpolation
  2 Feb 2024 1 repository listed
  In molecular dynamics simulations, rare events, such as protein folding, are typically studied using enhanced sampling techniques, most of which are based on the definition of a collective variable (CV) along which…
• A Study of Acquisition Functions for Medical Imaging Deep Active Learning
  28 Jan 2024 1 repository listed
  In this work, we show how active learning could be very effective in data scarcity situations, where obtaining labeled data (or annotation budget is very limited).
• Reassessing the Exon-Foldon correspondence using Frustration Analysis
  4 Jan 2024 1 repository listed
  Protein folding and evolution are intimately linked phenomena.
• Progressive Multi-Modality Learning for Inverse Protein Folding
  11 Dec 2023 1 repository listed
  While deep generative models show promise for learning inverse protein folding directly from data, the lack of publicly available structure-sequence pairings limits their generalization.
• Mega-scale experimental analysis of protein folding stability in biology and design
  19 Jul 2023 1 repository listed
  Here we present cDNA display proteolysis, a method for measuring thermodynamic folding stability for up to 900, 000 protein domains in a one-week experiment.
• Solvent: A Framework for Protein Folding
  7 Jul 2023 1 repository listed
  We hope that Solvent will increase the reliability and consistency of proposed models and give efficiency in both speed and costs, resulting in acceleration on protein folding modeling research.
• Graph Denoising Diffusion for Inverse Protein Folding
  29 Jun 2023 1 repository listed Syntology ran 11 of 21 samples · 10 unverified
  In contrast, diffusion probabilistic models, as an emerging genre of generative approaches, offer the potential to generate a diverse set of sequence candidates for determined protein backbones.
• Machine learning in and out of equilibrium
  6 Jun 2023 1 repository listed
  In an example system where the posterior is exactly known, this SGWORLD algorithm outperforms SGLD, converging to the posterior orders of magnitude faster as a function of the learning rate.
• Towards Expert-Level Medical Question Answering with Large Language Models
  16 May 2023 1 repository listed
  Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a…
• PS4: a Next-Generation Dataset for Protein Single Sequence Secondary Structure Prediction
  1 Mar 2023 1 repository listed
  Protein secondary structure prediction is a subproblem of protein folding.
• Pareto Dominance Archive and Coordinated Selection Strategy-Based Many-Objective Optimizer for Protein Structure Prediction
  22 Feb 2023 1 repository listed
  One of the efficient tools to describe this information is protein energy functions.
• Reinforcement Learning for Molecular Dynamics Optimization: A Stochastic Pontryagin Maximum Principle Approach
  6 Dec 2022 1 repository listed
  In this paper, we present a novel reinforcement learning framework designed to optimize molecular dynamics by focusing on the entire trajectory rather than just the final molecular configuration.
• Protein Language Models and Structure Prediction: Connection and Progression
  30 Nov 2022 1 repository listed
  The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding.

Syntology lines on 6 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.