{"total":53,"rows":[{"id":"2206.13517","title":"ProGen2: Exploring the Boundaries of Protein Language Models","created":"2022-06-27","cited_by_count":159,"area":null},{"id":"2203.12742","title":"Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders","created":"2022-03-23","cited_by_count":102,"area":null},{"id":"2208.06073","title":"Conditional Antibody Design as 3D Equivariant Graph Translation","created":"2022-08-12","cited_by_count":75,"area":null},{"id":"2303.11568","title":"Large AI Models in Health Informatics: Applications, Challenges, and the Future","created":"2023-03-21","cited_by_count":61,"area":null},{"id":"2401.06199","title":"xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein","created":"2024-01-11","cited_by_count":50,"area":null},{"id":"2302.00203","title":"End-to-End Full-Atom Antibody Design","created":"2023-02-01","cited_by_count":49,"area":null},{"id":"2308.05027","title":"AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies","created":"2023-07-28","cited_by_count":35,"area":"diffusion"},{"id":"2403.16576","title":"Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization","created":"2024-03-25","cited_by_count":30,"area":null},{"id":"2402.08703","title":"A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation","created":"2024-02-13","cited_by_count":29,"area":null},{"id":"2409.06744","title":"ProteinBench: A Holistic Evaluation of Protein Foundation Models","created":"2024-09-10","cited_by_count":25,"area":null},{"id":"2403.17889","title":"Large scale paired antibody language models","created":"2024-03-26","cited_by_count":16,"area":null},{"id":"2302.10888","title":"Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy","created":"2023-02-05","cited_by_count":10,"area":null},{"id":"2410.12459","title":"HELM: Hierarchical Encoding for mRNA Language Modeling","created":"2024-10-16","cited_by_count":10,"area":null},{"id":"2503.01910","title":"dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen","created":"2025-03-01","cited_by_count":10,"area":null},{"id":"2410.15040","title":"Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization","created":"2024-10-19","cited_by_count":9,"area":"diffusion"},{"id":"2506.20957","title":"Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Binding","created":"2025-06-26","cited_by_count":9,"area":"diffusion"},{"id":"2305.09480","title":"Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer","created":"2023-04-21","cited_by_count":8,"area":null},{"id":"2407.18184","title":"AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction","created":"2024-07-25","cited_by_count":8,"area":null},{"id":"2207.00982","title":"Linguistically inspired roadmap for building biologically reliable protein language models","created":"2022-07-03","cited_by_count":7,"area":null},{"id":"2501.10282","title":"Computational Protein Science in the Era of Large Language Models (LLMs)","created":"2025-01-17","cited_by_count":6,"area":null},{"id":"2301.12112","title":"On Pre-trained Language Models for Antibody","created":"2023-01-28","cited_by_count":4,"area":null},{"id":"2506.04235","title":"AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Design","created":"2025-05-23","cited_by_count":4,"area":null},{"id":"2211.08406","title":"Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design","created":"2022-10-26","cited_by_count":3,"area":null},{"id":"2306.03329","title":"AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions","created":"2023-06-06","cited_by_count":3,"area":null},{"id":"2405.18749","title":"A SARS-CoV-2 Interaction Dataset and VHH Sequence Corpus for Antibody Language Models","created":"2024-05-29","cited_by_count":3,"area":null},{"id":"2412.04737","title":"Generative Humanization for Therapeutic Antibodies","created":"2024-12-06","cited_by_count":3,"area":null},{"id":"2506.17857","title":"AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking","created":"2025-06-21","cited_by_count":3,"area":null},{"id":"2606.16905","title":"Speaking the Language of Science: Toward a General-Purpose Generative Foundation Model for the Natural Sciences","created":"2026-06-15","cited_by_count":3,"area":null},{"id":"2209.12635","title":"ImmunoLingo: Linguistics-based formalization of the antibody language","created":"2022-09-26","cited_by_count":2,"area":null},{"id":"2212.00735","title":"xTrimoABFold: De novo Antibody Structure Prediction without MSA","created":"2022-11-30","cited_by_count":2,"area":null},{"id":"2411.15215","title":"S$^2$ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning","created":"2024-11-20","cited_by_count":2,"area":null},{"id":"2502.10365","title":"AffinityFlow: Guided Flows for Antibody Affinity Maturation","created":"2025-02-14","cited_by_count":1,"area":null},{"id":"2604.11272","title":"AbLWR:A Context-Aware Listwise Ranking Framework for Antibody-Antigen Binding Affinity Prediction via Positive-Unlabeled Learning","created":"2026-04-13","cited_by_count":1,"area":null},{"id":"2307.04603","title":"Solvent: A Framework for Protein Folding","created":"2023-07-07","cited_by_count":0,"area":null},{"id":"2309.13129","title":"AntiBARTy Diffusion for Property Guided Antibody Design","created":"2023-09-22","cited_by_count":0,"area":null},{"id":"2401.14442","title":"Improving Antibody Humanness Prediction using Patent Data","created":"2024-01-25","cited_by_count":0,"area":null},{"id":"2402.05982","title":"Decoupled Sequence and Structure Generation for Realistic Antibody Design","created":"2024-02-08","cited_by_count":0,"area":null},{"id":"2412.01388","title":"Harnessing Preference Optimisation in Protein LMs for Hit Maturation in Cell Therapy","created":"2024-12-02","cited_by_count":0,"area":"alignment"},{"id":"2504.08437","title":"Customizing Spider Silk: Generative Models with Mechanical Property Conditioning for Protein Engineering","created":"2025-04-11","cited_by_count":0,"area":null},{"id":"2505.02022","title":"NbBench: Benchmarking Language Models for Comprehensive Nanobody Tasks","created":"2025-05-04","cited_by_count":0,"area":null},{"id":"2506.09052","title":"Llama-Affinity: A Predictive Antibody Antigen Binding Model Integrating Antibody Sequences with Llama3 Backbone Architecture","created":"2025-05-17","cited_by_count":0,"area":null},{"id":"2506.13006","title":"Antibody Foundational Model : Ab-RoBERTa","created":"2025-06-16","cited_by_count":0,"area":null},{"id":"2507.19805","title":"Sequence-based protein-protein interaction prediction and its applications in drug discovery","created":"2025-07-26","cited_by_count":0,"area":null},{"id":"2509.23254","title":"ABConformer: Physics-inspired Sliding Attention for Antibody-Antigen Interface Prediction","created":"2025-09-27","cited_by_count":0,"area":null},{"id":"2511.03113","title":"FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation","created":"2025-11-05","cited_by_count":0,"area":null},{"id":"2512.22007","title":"DuaDeep-SeqAffinity: Dual-Branch Deep Learning for Tri-Stream Sequence-Based Antibody--Antigen Affinity Prediction","created":"2025-12-26","cited_by_count":0,"area":null},{"id":"2602.18982","title":"Conditionally Site-Independent Neural Evolution of Antibody Sequences","created":"2026-02-21","cited_by_count":0,"area":null},{"id":"2604.09369","title":"Biologically-Grounded Multi-Encoder Architectures as Developability Oracles for Antibody Design","created":"2026-04-10","cited_by_count":0,"area":null},{"id":"2605.06720","title":"Conditional generation of antibody sequences with classifier-guided germline-absorbing discrete diffusion","created":"2026-05-07","cited_by_count":0,"area":"diffusion"},{"id":"2605.28886","title":"Computational Modeling of Antibody-Antigen Complexes: PLM-Based and MSA-Based Approaches","created":"2026-05-27","cited_by_count":0,"area":null},{"id":"2607.05846","title":"AbICL: In-Context Learning for Antigen-Specific Antibody Affinity Ranking","created":"2026-07-07","cited_by_count":0,"area":null},{"id":"2607.20057","title":"Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design","created":"2026-07-22","cited_by_count":0,"area":null},{"id":"2608.01092","title":"Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction","created":"2026-08-02","cited_by_count":0,"area":null}],"next_cursor":null}