Protein Language Model

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

1 leaderboard table shown for this task, 1 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

5 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.

Parent tasks archive 2025-07-28

Most implemented papers archive 2025-07-28

30 shown of 47 papers with code (73 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.

• ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling
  5 Mar 2024 2 repositories listed Syntology ran 1 of 3 samples · 2 unverified
  In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling.
• ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning
  1 Dec 2023 2 repositories listed
  Meanwhile, the ESM-NBR obtains the MCC values for DNA-binding residues prediction of 0.
• Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity
  21 Apr 2020 2 repositories listed
  Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer from the critical issue of mRNA instability and degradation, which is a major obstacle in the storage, distribution, and efficacy of the…
• AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking
  21 Jun 2025 1 repository listed
  Accurate prediction of antibody-antigen (Ab-Ag) binding affinity is essential for therapeutic design and vaccine development, yet the performance of current models is limited by noisy experimental labels, heterogeneous…
• Structure-Aligned Protein Language Model
  22 May 2025 1 repository listed
  Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but lack the structural knowledge essential for many biological applications.
• Leveraging Protein Language Model Embeddings for Catalytic Turnover Prediction of Adenylate Kinase Orthologs in a Low-Data Regime
  5 May 2025 1 repository listed
  Overall, this study assesses the state of the field for leveraging PLMs for sequence-to-k_(cat) prediction on a set of diverse ADK orthologs.
• Simulating 500 million years of evolution with a language model
  31 Dec 2024 1 repository listed
  Among the generations that we synthesized, we found a bright fluorescent protein at a far distance (58% sequence identity) from known fluorescent proteins, which we estimate is equivalent to simulating five hundred…
• Learning to engineer protein flexibility
  24 Dec 2024 1 repository listed Syntology ran 9 of 11 samples · 2 unverified
  Third, we introduce a method for fine-tuning a protein inverse folding model to steer it toward desired flexibility in specified regions.
• Comprehensive Assessment of BERT-Based Methods for Predicting Antimicrobial Peptides
  24 Dec 2024 1 repository listed
  Additionally, to explore the applicability and generalization ability of the models, we constructed a short peptide data set and an external data set to test the retrained models.
• Multi-Scale Representation Learning for Protein Fitness Prediction
  2 Dec 2024 1 repository listed Syntology ran 1 of 9 samples · 8 unverified
  Designing novel functional proteins crucially depends on accurately modeling their fitness landscape.
• Expert-guided protein language models enable accurate and blazingly fast fitness prediction
  22 Nov 2024 1 repository listed
  Results To overcome the sparsity of experimental training data, we created a dataset of 39 million single amino acid variants from the human proteome applying the multiple sequence alignment-based effect predictor GEMME…
• Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers
  29 Oct 2024 1 repository listed
  Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design.
• Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model
  28 Oct 2024 1 repository listed Syntology ran 1 of 5 samples · 4 unverified · 5 pointer-only (licence)
  Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other properties.
• 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.
• DPLM-2: A Multimodal Diffusion Protein Language Model
  17 Oct 2024 1 repository listed Syntology ran 2 of 2 samples · 0 unverified · 2 pointer-only (licence)
  In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures.
• Fine-tuning the ESM2 protein language model to understand the functional impact of missense variants
  14 Oct 2024 1 repository listed
  Elucidating the functional effect of missense variants is of crucial importance, yet challenging.
• DrugTar Improves Druggability Prediction by Integrating Large Language Models and Gene Ontologies
  24 Sep 2024 1 repository listed
  Moreover, the potential of raw sequence and protein structure has not been fully investigated.
• tcrLM: a lightweight protein language model for predicting T cell receptor and epitope binding specificity
  24 Jun 2024 1 repository listed
  These findings demonstrate the potential of tcrLM in predicting TCR-antigen binding specificity, with significant implications for advancing immunotherapy and personalized medicine.
• Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space
  29 May 2024 1 repository listed Syntology ran 3 of 3 samples · 0 unverified · 3 pointer-only (licence)
  Proteins are complex molecules responsible for different functions in nature.
• AntiFold: Improved antibody structure-based design using inverse folding
  6 May 2024 1 repository listed
  AntiFold outperforms existing inverse folding tools on sequence recovery across complementarity-determining regions, with designed sequences showing high structural similarity to their solved counterpart.
• Detection of circular permutations by Protein Language Models
  23 Apr 2024 1 repository listed
  Protein circular permutations are crucial for understanding protein evolution and functionality.
• AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides
  15 Apr 2024 1 repository listed
  This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids.
• On Recovering Higher-order Interactions from Protein Language Models
  15 Mar 2024 1 repository listed
  We demonstrate that ESM2 is dominated by three regions in the sparsity-ruggedness plane, two of which are better suited for sparse Fourier transforms.
• Diffusion Language Models Are Versatile Protein Learners
  28 Feb 2024 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences.
• Decoupled Sequence and Structure Generation for Realistic Antibody Design
  8 Feb 2024 1 repository listed
  A dominant paradigm is to train a model to jointly generate the antibody sequence and the structure as a candidate.
• Structure-Informed Protein Language Model
  7 Feb 2024 1 repository listed
  To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input.
• CrossBind: Collaborative Cross-Modal Identification of Protein Nucleic-Acid-Binding Residues
  19 Dec 2023 1 repository listed
  Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design.
• Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model
  14 Dec 2023 1 repository listed
  Signal peptide (SP) is a short peptide located in the N-terminus of proteins.
• PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications
  26 Oct 2023 1 repository listed
  Moreover, despite the wealth of benchmarks and studies in the natural language community, there remains a lack of a comprehensive benchmark for systematically evaluating protein language model quality.
• Cognate Transformer for Automated Phonological Reconstruction and Cognate Reflex Prediction
  11 Oct 2023 1 repository listed
  Phonological reconstruction is one of the central problems in historical linguistics where a proto-word of an ancestral language is determined from the observed cognate words of daughter languages.

Syntology lines on 7 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.