PNBind: Prediction of Nucleic Acid-Binding Sites Using Protein Structure and Protein Language Models.
PubMed / 2026 Oct 08
Structure generationProtein language modelsEnzymes and function
RESEARCH INDEX / CURATED DAILY
论文雷达
聚合期刊、预印本与学术搜索结果，按研究方向归档。相关性评分仅用于内部筛选，不在站内展示。
Structure Generation / 结构生成
54 PAPERS↗
RGI-Toolkit: Differentiable Restraints for Controllable Biomolecular Structure Prediction
bioRxiv / 2026-10-06
Structure generationExperimental validation
EdiProPred: Prediction of Edible Plant Tissue-Associated Proteins Using Large Language Models
bioRxiv / 2026-10-06
Structure generationProtein language models
trFlow: ultrafast all-atom protein conformational ensemble generation via conditional flow matching
bioRxiv / 2026-10-05
Structure generationExperimental validation
Molecular Dynamics Simulations Empowered De Novo Design of Binding Peptide for Enhanced Direct Bioelectrocatalytic Oxygen Reduction
ACS Catalysis / 2026-10-05
Structure generationProtein language modelsBinders and therapeuticsEnzymes and functionExperimental validation
Generating Structural Ensembles of Disordered Proteins with Diffusion Models
bioRxiv / 2026-10-04
Structure generationExperimental validation
pLM-HP: Peptide hormone prediction using pre-trained protein language model representations.
PubMed / 2026 Oct 02
Structure generationProtein language modelsBinders and therapeuticsEnzymes and functionExperimental validation
Progress in structure prediction and design of adaptive immune receptors.
PubMed / 2026 Oct 01
Structure generationSequence designBinders and therapeutics
What deep learning can and cannot (yet) do for enzyme design.
PubMed / 2026 Sep 30
Structure generationSequence designProtein language modelsEnzymes and function
De novo design of flexible protein interactions with GuideFlip
bioRxiv / 2026-09-30
Structure generationSequence designBinders and therapeuticsExperimental validation
AtomWeaver: Multi-Component Flow Matching with a Structured Geometric Prior Facilitates Non-Canonical Peptide Design
bioRxiv / 2026-09-28
Structure generationSequence designBinders and therapeuticsExperimental validation
Cerebra: a computationally efficient framework for accurate protein structure prediction
bioRxiv / 2026-09-26
Structure generationExperimental validation
Simplifying in silico protein evolution with minimal screening by unZipro.
PubMed / 2026 Sep 24
Structure generationSequence designEnzymes and functionExperimental validation
Intelligent De novo Design of Multifunctional Taste Peptides via an integrated deep learning, conditional diffusion, and reinforcement learning platform
Food Chemistry / 2026-09
Structure generation
Effective Sequence-to-Expression Prediction for a Model Membrane Protein Using Machine Learning and Computational Protein Design
ACS Synthetic Biology / 2026-09-23
Structure generationSequence designExperimental validation
Deep Learning-Guided Interface Engineering Stabilizes Oligomeric Enzymes
ACS Catalysis / 2026-09-21
Structure generationSequence designEnzymes and function
REAPS: An All-Atom Receptor-Aware Geometric Deep Learning Framework for De Novo Design of Linear and Macrocyclic Peptide Binders
Journal of Chemical Information and Modeling / 2026-09-19
Structure generationSequence designBinders and therapeuticsEnzymes and function
LLMsFold: Integrating Large Language Models and Biophysical Simulations for De Novo Drug Design
bioRxiv / 2026-09-18
Structure generationProtein language modelsBinders and therapeutics
BFVD v3-UniProt-complete, improved viral protein structure predictions
bioRxiv / 2026-09-18
Structure generation
Mechanistic Dissection of Conformational Transitions in a Bicyclic Peptide via Molecular Modeling and Deep Learning
Journal of Chemical Theory and Computation / 2026-09-15
Structure generationSequence designBinders and therapeuticsExperimental validation
ForceFlowAb: physics-aware mixture-of-experts flow matching model for antibody CDRs design
bioRxiv / 2026-09-14
Structure generationBinders and therapeutics
SpectroVQ: Noise-Aware Compression of Proteomics Data via Vector-Quantized Deep Learning improves MS/MS data storage and Peptide Identification
bioRxiv / 2026-09-11
Structure generationBinders and therapeutics
Predicting Capsid Protein Binding Sites in Single-Stranded RNA Viruses Using Machine Learning from Local Geometric Features
bioRxiv / 2026-09-11
Structure generationExperimental validation
Generative Language Modeling for Antibody CDR Grafting and Alignment-driven De Novo Design
bioRxiv / 2026-09-10
Structure generationBinders and therapeuticsEnzymes and functionExperimental validation
De novo design of allosterically controlled enzymes
bioRxiv / 2026-09-10
Structure generationEnzymes and function
Inverse FoldDir: Structure-conditioned Protein Sequence Design by Dirichlet Flow Matching
bioRxiv / 2026-09-11
Structure generationSequence designProtein language modelsEnzymes and functionExperimental validation
RFOptimization: Guiding Design Optimization with All-Atom Structure Prediction
Crossref / 2026-09-07
Structure generationSequence designBinders and therapeuticsEnzymes and function
Convergence Mechanisms of Generative Models in Molecular Conformational Sampling
Journal of Chemical Theory and Computation / 2026-09-07
Structure generationProtein language modelsBinders and therapeutics
Leveraging a Deep Learning Model and Computational Screening for the Discovery of ABCG2 Inhibitors against Drug-Resistant Breast Cancer
Journal of Chemical Information and Modeling / 2026-08-31
Structure generation
Design of peptides with non-canonical amino acids using flow matching
Bioinformatics / 2026-08-31
Structure generationBinders and therapeuticsEnzymes and function
Multilevel cytochrome P450 engineering integrating protein language model-guided evolution enables de novo biosynthesis of amentoflavone in Escherichia coli.
PubMed / 2026 Sep 01
Structure generationProtein language modelsEnzymes and functionExperimental validation
Bridging linguistic reasoning and biophysical reality toward peptide engineering via instruction-tuned language modeling.
PubMed / 2026 Aug 31
Structure generationSequence designProtein language modelsBinders and therapeuticsEnzymes and functionExperimental validation
A computational framework integrating a protein language model with alchemical simulation for gain-of-function enzyme design.
PubMed / 2026 Aug 31
Structure generationSequence designProtein language modelsBinders and therapeuticsEnzymes and function
De Novo Design of a Protein Binder to Probe Gas Channel and Enhance the Oxygen Tolerance of [NiFe]-Hydrogenase.
PubMed / 2026 Aug 26
Structure generationSequence designBinders and therapeuticsEnzymes and functionExperimental validation
AcrPLMEvo: A Two-Stage Framework Integrating Evolutionary Profiles with Protein Language Models for Anti-CRISPR Prediction.
PubMed / 2026 Aug 26
Structure generationProtein language models
HFGuidedDesign: de novo design of cyclic peptide binders via structure-guided discrete diffusion.
PubMed / 2026 Aug 19
Structure generationSequence designBinders and therapeutics
Synthetic sequence alignments as programmable probes of learned conformational landscapes in deep learning protein structure predictors.
PubMed / 2026 Aug 11
Structure generationSequence designEnzymes and function
Seed-Guided De Novo Design Expands the Structural Diversity of Antitoxin Protein Binders
biorxiv / 2026-08-04
Structure generationBinders and therapeuticsExperimental validation
GraESM-FuseDTA: adaptive gated multimodal fusion of graph neural networks and protein language models for robust drug-target affinity prediction.
PubMed / 2026 Aug 01
Structure generationProtein language modelsBinders and therapeutics
RINAMI: Residue-attributed interpretable neural network for predicting absolute folding free energy by merging structure and sequence information.
PubMed / 2026 Aug 01
Structure generationSequence designExperimental validation
PETIMOT: a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks.
PubMed / 2026 Aug 01
Structure generationProtein language modelsEnzymes and functionExperimental validation
Property guidance for protein sequence generative models with ProteinGuide.
PubMed / 2026 Jul 29
Structure generationSequence designExperimental validation
Structural and Stability Analysis of de Novo Designed Proteins Incorporating a Plant Self-Incompatibility Motif.
PubMed / 2026 Jul 24
Structure generationSequence designBinders and therapeuticsExperimental validation
Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer.
PubMed / 2026 Aug 06
Structure generationSequence designProtein language models
Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints
arXiv / 2026-07-20
Structure generation
An enzyme-specific protein language model for catalytic property prediction.
PubMed / 2026 Jul 17
Structure generationSequence designProtein language modelsEnzymes and functionExperimental validation
Fragment-based diffusion modeling and molecular dynamics simulation validation for the discovery of PD-L1 small-molecule inhibitors.
PubMed / 2026 Jul 17
Structure generationExperimental validation
De novo design of selective kinase modulators
Crossref / 2026-07-13
Structure generationBinders and therapeutics
Tightly coupled equivariant flow matching for molecular docking with multimodal physical constraints.
PubMed / 2026 Jul 09
Structure generation
TPS-Flow: Physics-Guided Flow-Based Generative Modeling of Protein Transition Paths.
PubMed / 2026 Jul 27
Structure generationEnzymes and function
PEPstrMOD2: Next-generation tertiary structure prediction of chemically modified and non-natural peptides
biorxiv / 2026-07-07
Structure generationBinders and therapeutics
BindRNAgen: Protein-binding RNA Sequence Generation Using Latent Diffusion Models.
PubMed / 2026 Oct 01
Structure generationProtein language modelsBinders and therapeuticsExperimental validation
Membrane protein solubilization and structure determination using de novo–designed proteins
Science / 2026-07-02
Structure generation
CFlowAMP: Property controllable De Novo AMP design via integrating ESM-2 with conditional flow matching.
PubMed / 2026 Jul 01
Structure generationProtein language modelsBinders and therapeuticsExperimental validation
Sequence Design / 序列设计
20 PAPERSIntegrating deep learning model for precision design of MERS antibodies with augmented affinity against SARS-CoV-2.
PubMed / 2026 Oct 06
Sequence designBinders and therapeuticsExperimental validation
Predicting Protein Thermostability with Equivariant Graph Neural Networks and Contrastive Learning
Journal of Chemical Information and Modeling / 2026-10-01
Sequence designProtein language modelsEnzymes and functionExperimental validation
SPLiNet: Lightweight prediction of protein-RNA interaction sites by integrating a structure-aware protein language model with a dual-branch network.
PubMed / 2026 Oct 01
Sequence designProtein language models
Integrating structural homology with deep learning to achieve highly accurate protein-protein interface prediction for the human interactome
bioRxiv / 2026-09-21
Sequence design
Codon language model scores provide information beyond protein language models for missense variant interpretation
bioRxiv / 2026-09-14
Sequence designProtein language models
Deep Learning-based Modeling Enhances Efficacy of Natural Ligand CAR Binders Targeting CD70
bioRxiv / 2026-09-10
Sequence designBinders and therapeuticsEnzymes and function
Mutation E300 recommended by protein language models gives ChrimsonR amplified photocurrent response
Sci Rep / 2026-09-08
Sequence designProtein language modelsEnzymes and function
De Novo Design and AlphaFold3 Evaluation of Protein Binders Targeting Specific Sites of MAP4K4
bioRxiv / 2026-09-07
Sequence designBinders and therapeuticsExperimental validation
Functional effect predictions for ion channel missense variants using a protein language model.
PubMed / 2026 Sep 01
Sequence designProtein language modelsEnzymes and function
Predicting Antibody–Antigen Mutation ΔΔ G via Side-Specific Protein Language Models and Paired Geometric Graph Learning
Journal of Chemical Information and Modeling / 2026-08-23
Sequence designProtein language modelsBinders and therapeuticsExperimental validation
EnerBridge-DPO: Energy-Aware Markov Bridge Inverse Folding for Protein Sequence Design.
PubMed / 2026 Aug 10
Sequence designExperimental validation
De novo design of proteinaceous binders targeting the LEDGF PWWP domain.
PubMed / 2026 Aug 01
Sequence designBinders and therapeuticsExperimental validation
Generative Machine Learning and Microfluidics uHTS: An Efficient Partnership for Enzyme Engineering
biorxiv / 2026-07-24
Sequence designEnzymes and functionExperimental validation
Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors.
biorxiv / 2026-07-21
Sequence design
Extending Protein Language Models to a Viral Genomic Scale Using Biologically Induced Sparse Attention.
PubMed / 2026 Jul 21
Sequence designProtein language modelsEnzymes and function
Artificial Intelligence and Protein Design: A retrospective study on 20-year emerging trends and core research areas from bibliometric perspectives.
PubMed / 2026 Jul 18
Sequence designBinders and therapeuticsExperimental validation
Understanding language model scaling for protein fitness prediction.
PubMed / 2026 Jul 13
Sequence designProtein language modelsEnzymes and function
Protein Language Model-Based Fitness Estimates Facilitate Resistance Mutation Identification.
PubMed / 2026 Jul 27
Sequence designProtein language modelsBinders and therapeuticsEnzymes and function
Prioritizing Stability-enhancing Mutations using the ESM Protein Language Model in conjunction with Physics-based MM/GBSA Predictions.
PubMed / 2026 Jul 06
Sequence designProtein language modelsExperimental validation
A deep mutational scanning-informed protein language model predicts SARS-CoV-2 evolution dynamics with spatiotemporal resolution.
PubMed / 2026 Jul 01
Sequence designProtein language models
Protein Language Models / 蛋白质语言模型
73 PAPERSCorrigendum to “AVP-GPT2: Prompt-conditioned fine-tuning of a GPT-2 protein language model for antiviral peptide identification” [Eur. J. Med. Chem. 320 (2026) 119352]
European Journal of Medicinal Chemistry / 2026-10
Protein language modelsBinders and therapeutics
LoRA-N-Gly: Sequence-based Prediction of N-Linked Glycosylation Sites by Tuning Protein Language Models with Low-rank Adaptation.
PubMed / 2026 Oct 08
Protein language models
Protein Language Model-Conditioned Graph Neural Networks for Multitask GPCR Ligand Activity Prediction
bioRxiv / 2026-10-07
Protein language models
Machine Learning Empowers Enzyme Discovery, Structure Prediction, Engineering, and Design
ACS Catalysis / 2026-10-07
Protein language modelsEnzymes and functionExperimental validation
ToxMamba: a novel method for toxic peptide prediction based on the fusion of pretrained embeddings and multi-scale state space models
Briefings in Bioinformatics / 2026-09-01
Protein language modelsBinders and therapeutics
AraVirusPPI: A protein language model-powered method for predicting Arabidopsis thaliana-virus protein-protein interactions.
PubMed / 2026 Oct 07
Protein language modelsExperimental validation
PepRePs: Peptide-Retargeted Phosphatases Designed with Generative Language Models
bioRxiv / 2026-10-06
Protein language modelsBinders and therapeutics
Mechanistic classification of the AAA superfamily with protein language models
bioRxiv / 2026-10-06
Protein language modelsEnzymes and function
DeepRAGIL-2: a retrieval-augmented protein language model framework for sensitive and accurate prediction of IL-2-inducing peptides.
PubMed / 2026 Oct 04
Protein language models
Generative modeling of intrinsically disordered protein regions by reinforcing sparse autoencoder features
arXiv / 2026-10-01
Protein language modelsEnzymes and function
AmyloCore-ML: AI/Machine Learning Enabled Identification of Amyloid Fibril Core Regions Using Protein Language Models
bioRxiv / 2026-10-01
Protein language modelsExperimental validation
A protein language model links the E. coli pangenome functional landscape geometry to host proteostasis
bioRxiv / 2026-09-30
Protein language modelsEnzymes and function
Interpreting embeddings from genome and protein language models.
PubMed / 2026 Oct 01
Protein language modelsEnzymes and function
Corrigendum to "SPLiNet: Lightweight prediction of protein-RNA interaction sites by integrating a structure-aware protein language model with a dual-branch network" [Comput. Biol. Chem. 124 (2026) 109130].
PubMed / 2026 Oct 01
Protein language models
Genome-wide-scale prediction of compound−protein interactions using foundation and language models based on three-dimensional structures of compounds and proteins
Bioinformatics / 2026-09-28
Protein language models
Evaluation of protein sequence retrieval via protein language model embeddings and FAISS
Computational Biology and Chemistry / 2026-09
Protein language models
ProMaya: A hierarchical universal deep learning framework for accurate and interpretable protein-protein interaction identification.
PubMed / 2026 Sep 24
Protein language models
PLM-ArgMe: Protein language model for arginine methylation prediction for different species.
PubMed / 2026 Sep 24
Protein language models
NRB-FusePS: A Protein Language Model-Based Multimodal Framework for Predicting Ligand-Binding Residues in Nuclear Receptors.
PubMed / 2026 Sep 23
Protein language models
AVP-GPT2: Prompt-Conditioned Fine-Tuning of a GPT-2 Protein Language Model for Antiviral Peptide Identification
European Journal of Medicinal Chemistry / 2026-09
Protein language modelsBinders and therapeutics
VirPLM: Antigenic prediction of influenza A/H3N2 viruses with a fine-tuned protein language model.
PubMed / 2026 Sep 18
Protein language models
Developing SCL2205: A Protein Sequence-based Spatial Modelling Dataset for the Protein Language Model Frontier.
PubMed / 2026 Sep 18
Protein language models
Explainable Artificial Intelligence to Unveil Patterns of Antioxidant Peptides for Free Radical Regulation
Journal of Chemical Information and Modeling / 2026-09-17
Protein language modelsBinders and therapeutics
Allosteric Pocket Prediction Based on Multi-modal Protein Language Models and Ensemble Learning.
PubMed / 2026 Sep 17
Protein language modelsEnzymes and function
ESpma: A method for assessing biological/non-biological interfaces using point-clouds-based structural features and protein language models.
PubMed / 2026 Oct 01
Protein language models
KRstereo: Predicting β-Hydroxy Stereochemistry in Polyketides Using Protein Language Models
Journal of Chemical Information and Modeling / 2026-09-16
Protein language modelsEnzymes and function
DeepEffector: A Protein Language Model-Driven Deep Learning Framework for Effector Prediction in Fungi and Oomycetes.
PubMed / 2026 Sep 16
Protein language modelsExperimental validation
Sampling protein language models for functional protein design
Cell Systems / 2026-09
Protein language models
A foundation model learns the sequence and functional grammar of fully human heavy-chain-only antibodies
bioRxiv / 2026-09-15
Protein language modelsBinders and therapeutics
LocPred-Prok: Prokaryotic protein subcellular localization prediction with a dual-branch architecture and protein language model.
PubMed / 2026 Sep 15
Protein language modelsEnzymes and function
DeepAlloWeb: a web server for interactive allosteric pockets prediction using protein language model.
PubMed / 2026 Sep 15
Protein language modelsEnzymes and function
OmniTCR: a foundation model unifying T cell receptor recognition prediction and conditional sequence generation
bioRxiv / 2026-09-13
Protein language modelsBinders and therapeutics
Agentic-AI-ready genome-wide poxvirus-host interaction screen refined by a protein language model
bioRxiv / 2026-09-13
Protein language modelsEnzymes and functionExperimental validation
ABCP_finder: A Transformer Embedding-Based Prediction of Anti-Breast Cancer Peptides
bioRxiv / 2026-09-13
Protein language modelsBinders and therapeutics
Functional alignment of protein language models via reinforcement learning
Nat Commun / 2026-09-12
Protein language models
Protein Language Model Embeddings Recover Evolutionary and Functional Organization Across the Ras Superfamily.
PubMed / 2026 Sep 12
Protein language models
BeitAI-pHLA: Multiallele Peptide-HLA Class I Binding Prediction Using Protein Language Model and Multi-Instance Learning.
PubMed / 2026 01 01
Protein language modelsBinders and therapeutics
ProteinSage: From implicit learning to explicit structural constraints for efficient protein language modeling
bioRxiv / 2026-09-09
Protein language models
De novo Rubisco design with protein language models
bioRxiv / 2026-09-09
Protein language modelsEnzymes and functionExperimental validation
NeoGen-BC: A synergistic framework combining generative protein language models and multi-window deep learning for designing shared neoantigens in breast cancer.
PubMed / 2026 Sep 09
Protein language modelsBinders and therapeutics
ProMaya: a hierarchical universal Deep Learning framework for accurate and interpretable Protein-Protein interaction identification
bioRxiv / 2026-09-08
Protein language models
Enhancing protein structure prediction accuracy by prioritizing important residues using protein language models
Commun Biol / 2026-09-08
Protein language models
Capsid-specialized protein language models reveal higher-order viral architecture from sequence
bioRxiv / 2026-09-07
Protein language models
AtlasFold: Protein structure prediction with metagenomic-scale language models
bioRxiv / 2026-09-07
Protein language modelsBinders and therapeutics
Protein Language Model Decoys for Target Decoy Competition in Proteomics: Quality Assessment and Benchmarks.
PubMed / 2026 Sep 04
Protein language modelsBinders and therapeutics
Retrieval-Augmented Residual Graph Neural Network for Protein-Protein Interaction Site Prediction.
PubMed / 2026 Sep 03
Protein language modelsEnzymes and functionExperimental validation
Unsupervised discovery of functional sequence patterns from protein language model with MotifAE
Nat Commun / 2026-09-02
Protein language models
Explainable attention-based multi-omics fusion with protein language models for CML-versus-control classification and biomarker discovery
Sci Rep / 2026-09-01
Protein language models
Semi-supervised Retrieval of Functional Residues Through the Integration of Protein Language Models and Gene Ontology Data
Bioinformatics / 2026-08-31
Protein language modelsEnzymes and functionExperimental validation
ESM2-Kcr: a novel model combining protein language model and deep learning methods for predicting lysine crotonylation sites.
PubMed / 2026 Aug 30
Protein language models
AI-enabled discovery and biochemical optimization of minibinders targeting cancer cell-surface proteins
Nat Commun / 2026-08-20
Protein language modelsBinders and therapeuticsExperimental validation
CLDN18.2 antibody design with protein language models: A deep learning optimization framework.
PubMed / 2026 Aug 20
Protein language modelsBinders and therapeuticsEnzymes and function
Enzyme Engineering: From Classical Strategies to AI-Driven Biocatalyst Design.
PubMed / 2026 Aug 19
Protein language modelsEnzymes and functionExperimental validation
Aligning protein-generative models to experimental fitness with ProteinDPO.
PubMed / 2026 Aug 14
Protein language modelsBinders and therapeuticsEnzymes and functionExperimental validation
Task- and dataset-specific information in protein language models
arXiv / 2026-08-12
Protein language models
How to Spend Your Oracle Budget: Practical Guidance for Protein Structure Prediction Models
arXiv / 2026-08-12
Protein language models
ARID-sf: A Physics-Informed Deep Learning Scoring Function to Improve Antibody-Antigen Docking Model Ranking.
PubMed / 2026 Aug 10
Protein language modelsBinders and therapeuticsEnzymes and function
The N-Terminus of Sophora tonkinensis Cytochrome P450s Evolves Neutrally yet Encodes Rich Functional Information: A Protein Language Model Analysis
biorxiv / 2026-08-06
Protein language modelsEnzymes and function
PlantPTM: A deep-learning framework integrating protein language models with multi-view features for predicting diverse post-translational modification sites in plants.
PubMed / 2026 Oct 05
Protein language models
Decoding the allosteric grammar of protein kinases: A dual-stream framework integrating protein language models and energy landscape frustration analysis.
PubMed / 2026 Aug 01
Protein language modelsBinders and therapeuticsEnzymes and function
ProtSyntax: a protein large language model for decoding post-translational modification syntax and function
biorxiv / 2026-07-21
Protein language modelsBinders and therapeuticsEnzymes and function
DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models
arXiv / 2026-07-21
Protein language modelsBinders and therapeutics
Leveraging protein language model for maturation of high-affinity peptide ligand in the purification of an adeno‒associated virus vector.
PubMed / 2026 Sep 27
Protein language modelsBinders and therapeutics
A Unified Molecular Graph and Protein Language Model Framework for Predicting Human Drug-Hormone Receptor Interactions with Structure-Aware Validation.
PubMed / 2026 Jul 27
Protein language modelsBinders and therapeuticsEnzymes and function
Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.
PubMed / 2026 Jul 28
Protein language models
Integrating Multi-View Residue Graph and Protein Language Model for Cell-Penetrating Peptide Prediction via Global-Local Graph Aggregation and Cross-Attentive Fusion.
PubMed / 2026 Jul 02
Protein language modelsBinders and therapeuticsEnzymes and functionExperimental validation
PEPE: scalable extraction of multi-modal protein language model representations.
PubMed / 2026 Jul 01
Protein language models
OTalign: Optimal Transport Alignment for Remote Protein Homologs Using Protein Language Model Embeddings.
PubMed / 2026 Jun 30
Protein language models
Prediction of cyclin-dependent proteins using pre-trained protein language models and effective neural network architectures.
PubMed / 2026 Jul 01
Protein language modelsBinders and therapeuticsExperimental validation
PCTPS: Accurate prediction of phase-separated proteins using protein language model embeddings and a CTN-KAN framework.
PubMed / 2026 Jul 01
Protein language models
Evaluating Protein Language Model Embeddings for Viral Clade Assignment.
PubMed / 2026 Jul 01
Protein language models
DeepSSInter: Protein-protein contact prediction with a structure-aware protein language model.
PubMed / 2026 Jul 01
Protein language modelsEnzymes and function
A PLM-based method for predicting protein ion channel modulators for drug discovery and safety evaluation.
PubMed / 2026 Jul 01
Protein language modelsBinders and therapeutics
Binders & Therapeutics / 结合蛋白与治疗
35 PAPERSValidation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition
Mol Syst Biol / 2026-10-08
Binders and therapeuticsEnzymes and function
Crowdsourcing functional cell therapy binders from generative artificial intelligence
Mol Syst Biol / 2026-10-08
Binders and therapeutics
Therapeutic peptide informatics in the artificial intelligence era: From curated resources to generative design
Drug Discovery Today / 2026-10
Binders and therapeutics
Machine Learning-Based Development of Gadolinium Binding Peptides.
PubMed / 2026 Oct 01
Binders and therapeuticsExperimental validation
Discriminating betacoronavirus receptor usage across subgenera using protein structure prediction and molecular dynamics
bioRxiv / 2026-09-28
Binders and therapeutics
A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions
Nat Commun / 2026-09-25
Binders and therapeutics
ARTIFICIAL INTELLIGENCE–BASED TOTAL METABOLIC TUMOUR VOLUME SEGMENTATION IN 18F-FDG PET/CT FOR CAR-T–TREATED DIFFUSE LARGE B- CELL LYMPHOMA: VALIDATION AND PERFORMANCE ASSESSMENT FOR CLINICAL INTEGRATION
Physica Medica / 2026-09
Binders and therapeutics
Artificial Intelligence in Food Bioactive Peptide Discovery: An Integrated Dual-Workflow for Predictive Screening and Generative Design, Advances, Challenges, and Future Directions
Food Bioscience / 2026-09
Binders and therapeutics
Programmed inhibition of an innate immune receptor via de novo designed transmembrane proteins
Proc. Natl. Acad. Sci. U.S.A. / 2026-09-29
Binders and therapeuticsEnzymes and function
Latent generative search unlocks de novo design of untapped biomolecular interactions at scale
bioRxiv / 2026-09-18
Binders and therapeutics
A Unified 3D Generative Model for Synthesizable Structure-Based Drug Design
bioRxiv / 2026-09-18
Binders and therapeuticsExperimental validation
De Novo Design of Miniprotein Inhibitors of Bacterial Adhesins
bioRxiv / 2026-09-16
Binders and therapeuticsEnzymes and function
An AI-Driven Chemogenomics Knowledgebase for Human-Transmissible Pathogens: A Platform for Antimicrobial Drug Discovery
Journal of Chemical Information and Modeling / 2026-09-15
Binders and therapeuticsExperimental validation
Antibody CDR-H3 loop flexibility: Insights from X-ray crystallography, structural bioinformatics, and the limits of current deep learning methods
Journal of Structural Biology / 2026-09
Binders and therapeutics
CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo
bioRxiv / 2026-09-12
Binders and therapeutics
Systematic Benchmarking of AlphaFold and SWISS-MODEL Kinase Structures for Structure-Based Drug Discovery
Journal of Molecular Graphics and Modelling / 2026-09
Binders and therapeutics
Chemical Descriptors and Deep Learning Embeddings for Scoring de novo Peptide Designs
bioRxiv / 2026-09-11
Binders and therapeutics
Artificial intelligence-assisted computational identification of peptide candidates against various key targets for combating hyperpigmentation and skin aging
Current Proteomics / 2026-08
Binders and therapeutics
Engineering conditional peptide self-assembly using AlphaFold
Cell Reports Physical Science / 2026-10
Binders and therapeutics
A geometry-over-coevolution principle governs protein complex assembly in AlphaFold
bioRxiv / 2026-09-08
Binders and therapeutics
De Novo Design of Targeted Drugs by Precisely Programming Multiple Molecular Binding
Journal of the American Chemical Society / 2026-09-07
Binders and therapeutics
Exploration of novel anti-TB agents targeting the serine/threonine kinase enzyme (PknE) in Mycobacterium tuberculosis: an in silico study
Sci Rep / 2026-09-05
Binders and therapeuticsEnzymes and functionExperimental validation
ABAG-Rank: Improving Model Selection of AlphaFold Antibody–Antigen Complexes by Learning to Rank
Bioinformatics / 2026-09-04
Binders and therapeutics
De novo designed single-domain antibodies protect against lethal cobra venom neurotoxicity in vivo
biorxiv / 2026-09-03
Binders and therapeuticsExperimental validation
De novo design of miniprotein drug conjugates targeting NECTIN-4 for cancer therapy
Acta Pharmaceutica Sinica B / 2026-09
Binders and therapeutics
Opportunities and challenges of artificial intelligence-driven peptide discovery
Chinese Chemical Letters / 2026-08
Binders and therapeutics
AI-Driven Drug–Target Interaction Prediction: From Data Representation to Model Design
Journal of Chemical Information and Modeling / 2026-08-21
Binders and therapeuticsExperimental validation
The sweet spot in protein design-Where deep learning meets first principles.
PubMed / 2026 Aug 10
Binders and therapeutics
Enhancing machine learning-based binder design with high-throughput screening: A comparison of mRNA and yeast display technologies.
PubMed / 2026 Aug 01
Binders and therapeuticsExperimental validation
Computational design of blue melanin by motif-scaffolding a pentapeptide-repeat protein.
PubMed / 2026 Aug 01
Binders and therapeutics
De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging.
PubMed / 2026 Aug 20
Binders and therapeutics
Hybrid quantum-classical de novo design of MHC-binding peptides
biorxiv / 2026-07-10
Binders and therapeutics
A High-Confidence Atlas of Protein Methylation Enables AI-Driven Detection of Methylated Peptides
biorxiv / 2026-07-04
Binders and therapeutics
AI-driven discovery of GPNMB CAR-T cells as a multi-cancer therapy
Cell / 2026
Binders and therapeutics
Structural feature-based machine learning benchmarking for protein interface prediction.
PubMed / 2026 Jun 27
Binders and therapeutics
Enzymes & Function / 酶与功能
9 PAPERSA molecular modeling and machine learning-based approach for the identification of potential human ALOX15 inhibitors.
PubMed / 2026 Sep 30
Enzymes and functionExperimental validation
Computational design of a versatile, zero-radius proximity labeling enzyme
bioRxiv / 2026-09-28
Enzymes and function
FoldMark: Safeguarding Protein Structure Generative Models with Distributional and Evolutionary Watermarking
bioRxiv / 2026-09-26
Enzymes and function
AlloPool is a deep learning framework that infers protein allostery from molecular dynamics simulations.
PubMed / 2026 Sep 01
Enzymes and functionExperimental validation
Deep Learning in Enzyme Function Prediction and Novel Enzyme Discovery
ACS Synthetic Biology / 2026-09-04
Enzymes and functionExperimental validation
From evolution to rational design: AI-driven engineering of safe and highly efficient food enzymes.
PubMed / 2026 Sep 01
Enzymes and functionExperimental validation
Generative artificial intelligence for enzyme design and biocatalysis.
PubMed / 2026 Oct 01
Enzymes and functionExperimental validation
Machine Learning for Microbial Cell Factories: Pathway Design, Enzyme Engineering, and Metabolic Regulation.
PubMed / 2026 Jul 17
Enzymes and function
EvoSeq-ML: Advancing Data-Centric Machine Learning with Evolutionary-Informed Protein Sequence Representation and Generation
biorxiv / 2026-06-27
Enzymes and function
Experimental Validation / 实验验证
4 PAPERS"EXPERT" A Practical and Forward-Looking Guide to Capturing Protein Expression and Purification Metadata to develop Machine Learning Models.
PubMed / 2026 Sep 29
Experimental validation
EM3DFold: accurate de novo protein and nucleic acid model building for cryo-EM maps using language model-powered deep learning
bioRxiv / 2026-09-18
Experimental validation
Machine Learning Models for Local Optimization of Red Fluorescent Protein Variants in a Low-Data Setting.
PubMed / 2026 Jul 27
Experimental validation
Transferable Implicit Solvent Machine Learning Potential for Drugs and Proteins Approaching Ab Initio Accuracy
arXiv / 2026-07-12
Experimental validation
General / 综合
22 PAPERSSIMORGH: Ensemble-Aware Geometric Deep Learning for Apo-State and Cryptic Ligand Binding Site Prediction
bioRxiv / 2026-10-08
General
Aptamers without SELEX: de novo design from protein structure in hours
Molecular Therapy Nucleic Acids / 2026-10
General
An AI-enabled proteome-scale framework for identifying sustainable protein alternatives for future food systems
npj Sci Food / 2026-10-08
General
WITHDRAWN: PredIDR3: A new output-encoding scheme and abundant negative source provide more information for deep learning-based protein intrinsic disorder prediction
bioRxiv / 2026-10-06
General
SN-PepDB: a deep learning-driven database for characterizing Sipunculus nudus bioactive peptides and their structure-activity relationships
Food Research International / 2026-10
General
Global analysis of thermal and chemical denaturation using CheMelt : Thermodynamic dissection of highly thermostable de novo designed proteins
Protein Science / 2026-11
General
Rhomboid tiling-based topological deep learning for protein complex structure quality assessment beyond pairwise contacts
Cell Reports Physical Science / 2026-10
General
De novo design of protein antagonists of bacterial pathogen type III secretion system needle assembly
Sci Rep / 2026-09-29
General
Sculpting semisynthetic conducting protein pores by de novo design
Nat Struct Mol Biol / 2026-09-22
General
PA-311 Multicentric Evaluation of SPIRIT IT: Artificial Intelligence to Detect and Characterize M-Protein
Clinical Lymphoma Myeloma and Leukemia / 2026-09
General
Generating protein hydrogels with customizable stress relaxation behavior via deep learning-driven entanglement design
Nat Commun / 2026-09-21
General
DeepGVS: a bimodal deep learning framework integrating coding-sequence and protein-structural representations for virulence factor prediction
Bioinformatics / 2026-09-21
General
REPLY-LETTER TO EDITOR/COMMENT ON: “Nutritional impact of leucine-enriched supplements: evaluating protein type through artificial intelligence (AI)-augmented muscle ultrasonography in hypercaloric, hyperproteic support”
Clinical Nutrition ESPEN / 2026-09
General
LGBind: A Structure-Guided Deep Learning Framework for Accurate Prediction of Protein-Ligand Binding Sites
European Journal of Medicinal Chemistry / 2026-09
General
Machine learning reveals sequence and genomic context features underlying Alu-specific effects on genome folding
bioRxiv / 2026-09-18
General
Rapid Assessment of Size, Shape, and Chemical Complementarity of Ligands for Computational Protein Design
bioRxiv / 2026-09-16
General
Systematic Optimization of Komagataella phaffii (Pichia pastoris) for High-Efficiency Recombinant Protein Production: Advancements in Strain Engineering, Fermentation Optimization, and AI-Driven Technologies
Engineering Microbiology / 2026-09
General
Metabolic engineering and deep learning-driven protein engineering for N-Acetylneuraminic acid biosynthesis in Escherichia coli
Nat Commun / 2026-09-05
General
Mapping the combinatorial coding between olfactory receptors and perception with deep learning.
PubMed / 2026 Sep 16
General
A systematic evaluation of deep learning-based protein structure prediction for HIV-1 enzymes
Sci Rep / 2026-08-27
General
AI-Guided De Novo Design of a Caffeine-Induced Protein Dissociation System.
PubMed / 2026 Jul 15
General