Protein Secondary Structure Prediction

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

8 leaderboard tables shown for this task, 8 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

1 dataset 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

13 shown of 13 papers with code (26 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.

• 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.
• 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.
• High Quality Prediction of Protein Q8 Secondary Structure by Diverse Neural Network Architectures
  17 Nov 2018 2 repositories listed
  In the spirit of reproducible research we make our data, models and code available, aiming to set a gold standard for purity of training and testing sets.
• 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.
• Convolutional ProteinUnetLM competitive with long short-term memory-based protein secondary structure predictors
  30 Nov 2022 1 repository listed
  In recent years, a new generation of algorithms for SS prediction based on embeddings from protein language models (pLMs) is emerging.
• DistilProtBert: A distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts
  10 May 2022 1 repository listed
  Here, we adapted this concept to the problem of protein sequence analysis, by developing DistilProtBert, a distilled version of the successful ProtBert model.
• DLPAlign: A Deep Learning based Progressive Alignment Method for Multiple Protein Sequences
  21 Nov 2020 1 repository listed
  This paper proposed a novel and straightforward approach to improve the accuracy of progressive multiple protein sequence alignment method.
• ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing
  13 Jul 2020 1 repository listed Syntology ran 0 of 3 samples · 3 unverified
  Here, we trained two auto-regressive models (Transformer-XL, XLNet) and four auto-encoder models (BERT, Albert, Electra, T5) on data from UniRef and BFD containing up to 393 billion amino acids.
• Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction
  12 Oct 2019 1 repository listed
  In spite of this, even the most sophisticated ab initio SS predictors are not able to reach the theoretical limit of three-state prediction accuracy (88–90%), while only a few predict more than the 3 traditional Helix,…
• Porter 5: fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
  5 Oct 2018 1 repository listed
  Motivation: Although secondary structure predictors have been developed for decades, current ab initio methods have still some way to go to reach their theoretical limits.
• Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks
  25 Apr 2016 1 repository listed
  Inspired by the recent successes of deep neural networks, in this paper, we propose an end-to-end deep network that predicts protein secondary structures from integrated local and global contextual features.
• Protein secondary structure prediction using deep convolutional neural fields
  2 Dec 2015 1 repository listed Syntology ran 0 of 3 samples · 3 unverified
  Protein secondary structure (SS) prediction is important for studying protein structure and function.
• Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction
  6 Mar 2014 1 repository listed
  Here we present a new supervised generative stochastic network (GSN) based method to predict local secondary structure with deep hierarchical representations.

Syntology lines on 3 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.