Protein Structure Prediction

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

4 leaderboard tables shown for this task, 4 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

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

Subtasks archive 2025-07-28

2 subtasks in the archive's task tree.

Most implemented papers archive 2025-07-28

30 shown of 67 papers with code (188 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.

• 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.
• SE(3) diffusion model with application to protein backbone generation
  5 Feb 2023 3 repositories listed Syntology ran 1 of 1 samples · 0 unverified · 1 pointer-only (licence)
  The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry.
• Distribution-Free, Risk-Controlling Prediction Sets
  7 Jan 2021 3 repositories listed Syntology ran 3 of 3 samples · 0 unverified
  While improving prediction accuracy has been the focus of machine learning in recent years, this alone does not suffice for reliable decision-making.
• SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning
  16 Oct 2020 3 repositories listed Syntology ran 4 of 12 samples · 8 unverified
  Despite recent advancements in deep learning methods for protein structure prediction and representation, little focus has been directed at the simultaneous inclusion and prediction of protein backbone and sidechain…
• Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations
  9 Nov 2019 3 repositories listed
  Our dataset consists of amino acid sequences, Q8 secondary structures, position specific scoring matrices, multiple sequence alignment co-evolutionary features, backbone atom distance matrices, torsion angles, and 3D…
• MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Protein Structure Prediction
  10 May 2016 3 repositories listed
  Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics.
• AtomSurf : Surface Representation for Learning on Protein Structures
  28 Sep 2023 2 repositories listed Syntology ran 13 of 16 samples · 3 unverified · 15 pointer-only (licence)
  In particular, there is a lack of direct and fair benchmark comparison between the best available surface-based learning methods against alternative representations such as graphs.
• 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.
• 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.
• PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction
  24 Jun 2022 2 repositories listed
  We provide in addition the benchmark training procedure for SOTA protein structure prediction model on this dataset.
• ProteinBERT: a universal deep-learning model of protein sequence and function
  10 Feb 2022 2 repositories listed
  We introduce ProteinBERT, a deep language model specifically designed for proteins.
• Iterative SE(3)-Transformers
  26 Feb 2021 2 repositories listed Syntology ran 3 of 3 samples · 0 unverified · 2 pointer-only (licence)
  Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data.
• ProteinNet: a standardized data set for machine learning of protein structure
  1 Feb 2019 2 repositories listed Syntology ran 0 of 7 samples · 7 unverified
  We have created the ProteinNet series of data sets to provide a standardized mechanism for training and assessing data-driven models of protein sequence-structure relationships.
• Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins
  11 Jul 2025 1 repository listed
  We introduce Ibex, a pan-immunoglobulin structure prediction model that achieves state-of-the-art accuracy in modeling the variable domains of antibodies, nanobodies, and T-cell receptors.
• 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.
• 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…
• Towards Interpretable Protein Structure Prediction with Sparse Autoencoders
  11 Mar 2025 1 repository listed Syntology ran 3 of 4 samples · 1 unverified · 4 pointer-only (licence)
  While sparse autoencoders (SAEs) offer a path to interpretability here by learning linear representations in high-dimensional space, their application has been limited to smaller protein language models unable to…
• Protein Large Language Models: A Comprehensive Survey
  21 Feb 2025 1 repository listed
  Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design.
• 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…
• Deep Learning of Proteins with Local and Global Regions of Disorder
  17 Feb 2025 1 repository listed
  Although machine learning has transformed protein structure prediction of folded protein ground states with remarkable accuracy, intrinsically disordered proteins and regions (IDPs/IDRs) are defined by diverse and…
• 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.
• Human Genome Book: Words, Sentences and Paragraphs
  23 Jan 2025 1 repository listed
  Using this model, we constructed a vocabulary of DNA words and mapped DNA words to their English equivalents.
• Generative diffusion model with inverse renormalization group flows
  15 Jan 2025 1 repository listed
  Here we introduce a renormalization group-based diffusion model that leverages multiscale nature of data distributions for realizing a high-quality data generation.
• Training on test proteins improves fitness, structure, and function prediction
  4 Nov 2024 1 repository listed
  Data scarcity and distribution shifts often hinder the ability of machine learning models to generalize when applied to proteins and other biological data.
• FoldMark: Protecting Protein Generative Models with Watermarking
  27 Oct 2024 1 repository listed
  Protein structure is key to understanding protein function and is essential for progress in bioengineering, drug discovery, and molecular biology.
• CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation
  21 Oct 2024 1 repository listed
  Building on works in structure prediction, We developed a structure-sensitive supervised deep learning model, Crystal vs Predicted Evaluator for Protein Structure (CPE-Pro), to represent and discriminate the origin of…
• pLDDT-Predictor: High-speed Protein Screening Using Transformer and ESM2
  11 Oct 2024 1 repository listed
  Recent advancements in protein structure prediction, particularly AlphaFold2, have revolutionized structural biology by achieving near-experimental accuracy (average RMSD < 1.
• DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
  2 Oct 2024 1 repository listed
  Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions.
• MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training
  8 Jun 2024 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families.

Syntology lines on 9 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.