Research graph
References from REAPS: An All-Atom Receptor-Aware Geometric Deep Learning Framework for <i>De Novo</i> Design of Linear and Macrocyclic Peptide Binders. Local targets link to admitted publications; unresolved targets remain external evidence.
Peptides as Therapeutic Agents: Challenges and Opportunities in the Green Transition Era
10.3390/molecules28207165 · 2023 · External reference
Robust deep learning–based protein sequence design using ProteinMPNN
10.1126/science.add2187 · 2022 · External reference
Learning inverse folding from millions of predicted structures
10.1101/2022.04.10.487779 · 2022 · External reference
Generative models for graph-based protein design
2019 · External reference
Learning from Protein Structure with Geometric Vector Perceptrons
10.48550/arxiv.2009.01411 · 2020 · External reference
PiFold: Toward effective and efficient protein inverse folding
10.48550/arxiv.2209.12643 · 2022 · External reference
Graph Denoising Diffusion for Inverse Protein Folding
10.48550/arxiv.2306.16819 · 2023 · External reference
Structure-informed Language Models Are Protein Designers
10.48550/arxiv.2302.01649 · 2023 · External reference
Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement
10.48550/arxiv.2305.15151 · 2023 · External reference
Mask-prior-guided denoising diffusion improves inverse protein folding
10.1038/s42256-025-01042-6 · 2025 · External reference
UniIF: Unified Molecule Inverse Folding
10.48550/arxiv.2405.18968 · 2024 · External reference
Bridge-IF: Learning Inverse Protein Folding with Markov Bridges
10.48550/arxiv.2411.02120 · 2024 · External reference
Atomic context-conditioned protein sequence design using LigandMPNN
10.1038/s41592-025-02626-1 · 2025 · External reference
Enhancing functional proteins through multimodal inverse folding with ABACUS-T
10.1038/s41467-025-65175-3 · 2025 · External reference
Improved De Novo Peptide Binder Design with Target-Conditioned Inverse Folding
10.1101/2025.10.28.685072 · 2025 · External reference
HighMPNN: A Graph Neural Network Approach for Structure-Constrained Cyclic Peptide Sequence Design
10.1109/jbhi.2025.3620163 · 2026 · External reference
CyclicMPNN: Stable Cyclic Peptide Sequence Generation
10.64898/2026.01.31.702993 · 2026 · External reference
The Protein Data Bank
10.1093/nar/28.1.235 · 2000 · External reference
PPFlow: Target-aware Peptide Design with Torsional Flow Matching
10.48550/arxiv.2405.06642 · 2024 · External reference
CPSea: Large-scale cyclic peptide-protein complex dataset for machine learning in cyclic peptide design
2026 · External reference
Predicting protein-protein interactions in the human proteome
10.1126/science.adt1630 · 2025 · External reference
PepBDB: a comprehensive structural database of biological peptide–protein interactions
10.1093/bioinformatics/bty579 · 2019 · External reference
Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures
10.3389/fbinf.2023.1103103 · 2023 · External reference
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions
10.1093/gpbjnl/qzae001 · 2024 · External reference
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
10.1038/nbt.3988 · 2017 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints
10.1093/bib/bbae215 · 2024 · External reference
Accurate de novo design of high-affinity protein-binding macrocycles using deep learning
10.1038/s41589-025-01929-w · 2025 · External reference
Cyclic peptide structure prediction and design using AlphaFold2
10.1038/s41467-025-59940-7 · 2025 · External reference
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
10.1021/acs.jctc.7b00125 · 2017 · External reference
Macromolecular modeling and design in Rosetta: recent methods and frameworks
10.1038/s41592-020-0848-2 · 2020 · External reference
ColabFold: making protein folding accessible to all
10.1038/s41592-022-01488-1 · 2022 · External reference
Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction
10.1101/2025.06.14.659707 · 2025 · External reference
Language Modeling Materializes a World Model of Protein Biology
10.64898/2026.06.03.729735 · 2026 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Protein complex prediction with AlphaFold-Multimer
10.1101/2021.10.04.463034 · 2021 · External reference
Amino acid substitution matrices from protein blocks
10.1073/pnas.89.22.10915 · 1992 · External reference
DockQ: A Quality Measure for Protein-Protein Docking Models
10.1371/journal.pone.0161879 · 2016 · External reference
Fast and accurate protein structure search with Foldseek
10.1038/s41587-023-01773-0 · 2024 · External reference
Scoring function for automated assessment of protein structure template quality
10.1002/prot.20264 · 2004 · External reference
How significant is a protein structure similarity with TM-score = 0.5?
10.1093/bioinformatics/btq066 · 2010 · External reference
Chai-1: Decoding the molecular interactions of life
10.1101/2024.10.10.615955 · 2024 · External reference
Boltz-1 Democratizing Biomolecular Interaction Modeling
10.1101/2024.11.19.624167 · 2024 · External reference
Have protein-ligand co-folding methods moved beyond memorisation?
10.1101/2025.02.03.636309 · 2025 · External reference
How AlphaFold and related models predict protein-peptide complex structures
10.1101/2025.06.18.660495 · 2025 · External reference
Protein Hunter: exploiting structure hallucination within diffusion for protein design
10.1101/2025.10.10.681530 · 2025 · External reference
HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence Design
10.1101/2025.11.08.686881 · 2026 · External reference
Modulation of body temperature and LH secretion by hypothalamic KNDy (kisspeptin, neurokinin B and dynorphin) neurons: A novel hypothesis on the mechanism of hot flushes
10.1016/j.yfrne.2013.07.003 · 2013 · External reference
Structural insights into neurokinin 3 receptor activation by endogenous and analogue peptide agonists
10.1038/s41421-023-00564-w · 2023 · External reference
Scoring function for automated assessment of protein structure template quality
10.1002/prot.20264 · ExternalCitation · doi-reference
Modulation of body temperature and LH secretion by hypothalamic KNDy (kisspeptin, neurokinin B and dynorphin) neurons: A novel hypothesis on the mechanism of hot flushes
10.1016/j.yfrne.2013.07.003 · ExternalCitation · doi-reference
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
10.1021/acs.jctc.7b00125 · ExternalCitation · doi-reference
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
10.1038/nbt.3988 · ExternalCitation · doi-reference
Structural insights into neurokinin 3 receptor activation by endogenous and analogue peptide agonists
10.1038/s41421-023-00564-w · ExternalCitation · doi-reference
Cyclic peptide structure prediction and design using AlphaFold2
10.1038/s41467-025-59940-7 · ExternalCitation · doi-reference
Enhancing functional proteins through multimodal inverse folding with ABACUS-T
10.1038/s41467-025-65175-3 · ExternalCitation · doi-reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · ExternalCitation · doi-reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · ExternalCitation · doi-reference
Fast and accurate protein structure search with Foldseek
10.1038/s41587-023-01773-0 · ExternalCitation · doi-reference
Accurate de novo design of high-affinity protein-binding macrocycles using deep learning
10.1038/s41589-025-01929-w · ExternalCitation · doi-reference
Macromolecular modeling and design in Rosetta: recent methods and frameworks
10.1038/s41592-020-0848-2 · ExternalCitation · doi-reference
ColabFold: making protein folding accessible to all
10.1038/s41592-022-01488-1 · ExternalCitation · doi-reference
Atomic context-conditioned protein sequence design using LigandMPNN
10.1038/s41592-025-02626-1 · ExternalCitation · doi-reference
Mask-prior-guided denoising diffusion improves inverse protein folding
10.1038/s42256-025-01042-6 · ExternalCitation · doi-reference
Amino acid substitution matrices from protein blocks
10.1073/pnas.89.22.10915 · ExternalCitation · doi-reference
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints
10.1093/bib/bbae215 · ExternalCitation · doi-reference
How significant is a protein structure similarity with TM-score = 0.5?
10.1093/bioinformatics/btq066 · ExternalCitation · doi-reference
PepBDB: a comprehensive structural database of biological peptide–protein interactions
10.1093/bioinformatics/bty579 · ExternalCitation · doi-reference
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions
10.1093/gpbjnl/qzae001 · ExternalCitation · doi-reference
The Protein Data Bank
10.1093/nar/28.1.235 · ExternalCitation · doi-reference
Protein complex prediction with AlphaFold-Multimer
10.1101/2021.10.04.463034 · ExternalCitation · doi-reference
Learning inverse folding from millions of predicted structures
10.1101/2022.04.10.487779 · ExternalCitation · doi-reference
Chai-1: Decoding the molecular interactions of life
10.1101/2024.10.10.615955 · ExternalCitation · doi-reference
Boltz-1 Democratizing Biomolecular Interaction Modeling
10.1101/2024.11.19.624167 · ExternalCitation · doi-reference
Have protein-ligand co-folding methods moved beyond memorisation?
10.1101/2025.02.03.636309 · ExternalCitation · doi-reference
Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction
10.1101/2025.06.14.659707 · ExternalCitation · doi-reference
How AlphaFold and related models predict protein-peptide complex structures
10.1101/2025.06.18.660495 · ExternalCitation · doi-reference
Protein Hunter: exploiting structure hallucination within diffusion for protein design
10.1101/2025.10.10.681530 · ExternalCitation · doi-reference
Improved De Novo Peptide Binder Design with Target-Conditioned Inverse Folding
10.1101/2025.10.28.685072 · ExternalCitation · doi-reference
HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence Design
10.1101/2025.11.08.686881 · ExternalCitation · doi-reference
HighMPNN: A Graph Neural Network Approach for Structure-Constrained Cyclic Peptide Sequence Design
10.1109/jbhi.2025.3620163 · ExternalCitation · doi-reference
Robust deep learning–based protein sequence design using ProteinMPNN
10.1126/science.add2187 · ExternalCitation · doi-reference
Predicting protein-protein interactions in the human proteome
10.1126/science.adt1630 · ExternalCitation · doi-reference
DockQ: A Quality Measure for Protein-Protein Docking Models
10.1371/journal.pone.0161879 · ExternalCitation · doi-reference
Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures
10.3389/fbinf.2023.1103103 · ExternalCitation · doi-reference
Peptides as Therapeutic Agents: Challenges and Opportunities in the Green Transition Era
10.3390/molecules28207165 · ExternalCitation · doi-reference
Learning from Protein Structure with Geometric Vector Perceptrons
10.48550/arxiv.2009.01411 · ExternalCitation · doi-reference
PiFold: Toward effective and efficient protein inverse folding
10.48550/arxiv.2209.12643 · ExternalCitation · doi-reference
Structure-informed Language Models Are Protein Designers
10.48550/arxiv.2302.01649 · ExternalCitation · doi-reference
Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement
10.48550/arxiv.2305.15151 · ExternalCitation · doi-reference
Graph Denoising Diffusion for Inverse Protein Folding
10.48550/arxiv.2306.16819 · ExternalCitation · doi-reference
PPFlow: Target-aware Peptide Design with Torsional Flow Matching
10.48550/arxiv.2405.06642 · ExternalCitation · doi-reference
UniIF: Unified Molecule Inverse Folding
10.48550/arxiv.2405.18968 · ExternalCitation · doi-reference
Bridge-IF: Learning Inverse Protein Folding with Markov Bridges
10.48550/arxiv.2411.02120 · ExternalCitation · doi-reference
CyclicMPNN: Stable Cyclic Peptide Sequence Generation
10.64898/2026.01.31.702993 · ExternalCitation · doi-reference
Language Modeling Materializes a World Model of Protein Biology
10.64898/2026.06.03.729735 · ExternalCitation · doi-reference
