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Drug Design

Papers archive 2025-07-28

archive papers tagged: 440 · with a code link: 180 · where Syntology ran a sample: 66 (58 with a run with no instrument failure, 8 where every run was a failure of Syntology's instrument) Syntology

Show: all tagged papersonly where code ran (66 of 440 tagged: 58 with a run with no instrument failure, 8 where every run was a failure of Syntology's instrument)

Page 2 of 5: papers 101 to 200 of 440, in archive order: by repositories listed in the archive (most first), then newest first, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers that list no repository come after every paper that lists one.

Papers without a page here are shown as plain text. A Syntology line reads “N ran (of which C constructed an object rather than computing a result; K with no instrument failure: H honoured, V violated, P with no contract checked; I where Syntology's instrument failed) · U unverified”; the figure “where Syntology's instrument failed” counts failures of Syntology's instrument, not of the code. When the archive marks a repository official for the paper, the line starts with that repository's state (the archive's flag, not a verdict on who wrote the code); hover it for the repositories the samples that ran came from. Abstracts are on each paper's page.

• Learning big logical rules by joining small rules
  29 Jan 2024 1 repository listed Syntology official (archive's flag): 13 ran · 13 ran (of which 0 constructed an object rather than computing a result; 13 with no instrument failure: 0 honoured, 0 violated, 13 with no contract checked; 0 where Syntology's instrument failed) · 4 unverified (of 17 harvested samples) · 17 pointer-only (licence)
• Endowing Protein Language Models with Structural Knowledge
  26 Jan 2024 1 repository listed
• DeepRLI: A Multi-objective Framework for Universal Protein--Ligand Interaction Prediction
  19 Jan 2024 1 repository listed
• Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction
  17 Jan 2024 1 repository listed Syntology official (archive's flag): 1 ran · 1 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified (of 1 harvested sample)
• Binding-Adaptive Diffusion Models for Structure-Based Drug Design
  15 Jan 2024 1 repository listed Syntology official (archive's flag): 9 ran · 9 ran (of which 0 constructed an object rather than computing a result; 8 with no instrument failure: 2 honoured, 0 violated, 6 with no contract checked; 1 where Syntology's instrument failed) · 2 unverified (of 11 harvested samples) · 11 pointer-only (licence)
• Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs
  15 Jan 2024 1 repository listed
• CrossBind: Collaborative Cross-Modal Identification of Protein Nucleic-Acid-Binding Residues
  19 Dec 2023 1 repository listed
• NovoMol: Recurrent Neural Network for Orally Bioavailable Drug Design and Validation on PDGFRα Receptor
  3 Dec 2023 1 repository listed
• DiffBindFR: An SE(3) Equivariant Network for Flexible Protein-Ligand Docking
  26 Nov 2023 1 repository listed Syntology official (archive's flag): 13 ran · 13 ran (of which 0 constructed an object rather than computing a result; 13 with no instrument failure: 0 honoured, 0 violated, 13 with no contract checked; 0 where Syntology's instrument failed) · 2 unverified (of 15 harvested samples) · 15 pointer-only (licence)
• Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
  22 Nov 2023 1 repository listed Syntology official (archive's flag): 1 ran · 1 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 0 where Syntology's instrument failed) · 3 unverified (of 4 harvested samples)
• ProFSA: Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment
  11 Oct 2023 1 repository listed Syntology 3 ran (of which 0 constructed an object rather than computing a result; 3 with no instrument failure: 0 honoured, 0 violated, 3 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified (of 3 harvested samples)
• Curiosity as a Self-Supervised Method to Improve Exploration in De novo Drug Design
  24 Sep 2023 1 repository listed
• GGL-PPI: Geometric Graph Learning to Predict Mutation-Induced Binding Free Energy Changes
  23 Sep 2023 1 repository listed
• Structure to Property: Chemical Element Embeddings and a Deep Learning Approach for Accurate Prediction of Chemical Properties
  17 Sep 2023 1 repository listed
• Learning MDL logic programs from noisy data
  18 Aug 2023 1 repository listed Syntology official (archive's flag): 13 ran · 13 ran (of which 0 constructed an object rather than computing a result; 13 with no instrument failure: 0 honoured, 0 violated, 13 with no contract checked; 0 where Syntology's instrument failed) · 3 unverified (of 16 harvested samples) · 16 pointer-only (licence)
• DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping
  14 Aug 2023 1 repository listed Syntology official (archive's flag): 1 ran · 1 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 0 honoured, 1 violated, 0 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified (of 1 harvested sample)
• Protein-DNA binding sites prediction based on pre-trained protein language model and contrastive learning
  28 Jun 2023 1 repository listed
• Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop
  22 Jun 2023 1 repository listed
• GEO-Nav: a geometric dataset of voltage-gated sodium channels
  21 Jun 2023 1 repository listed
• Geometric Deep Learning for Structure-Based Drug Design: A Survey
  20 Jun 2023 1 repository listed
• Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration
  30 May 2023 1 repository listed
• Learning Subpocket Prototypes for Generalizable Structure-based Drug Design
  22 May 2023 1 repository listed Syntology community repositories only · 1 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 1 unverified (of 2 harvested samples) · 2 pointer-only (licence)
• O-GNN: Incorporating Ring Priors into Molecular Modeling
  1 May 2023 1 repository listed
• SILVR: Guided Diffusion for Molecule Generation
  21 Apr 2023 1 repository listed
• An Equivariant Generative Framework for Molecular Graph-Structure Co-Design
  12 Apr 2023 1 repository listed Syntology official (archive's flag): 4 ran · 4 ran (of which 0 constructed an object rather than computing a result; 2 with no instrument failure: 2 honoured, 0 violated, 0 with no contract checked; 2 where Syntology's instrument failed) · 2 unverified (of 6 harvested samples) · 5 pointer-only (licence)
• Utilizing Reinforcement Learning for de novo Drug Design
  30 Mar 2023 1 repository listed
• Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Model
  13 Mar 2023 1 repository listed
• DP-Fast MH: Private, Fast, and Accurate Metropolis-Hastings for Large-Scale Bayesian Inference
  10 Mar 2023 1 repository listed
• ClaPIM: Scalable Sequence CLAssification using Processing-In-Memory
  16 Feb 2023 1 repository listed
• Domain-Agnostic Molecular Generation with Chemical Feedback
  26 Jan 2023 1 repository listed Syntology official (archive's flag): 5 ran · 5 ran (of which 0 constructed an object rather than computing a result; 3 with no instrument failure: 0 honoured, 0 violated, 3 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified (of 5 harvested samples) · 2 pointer-only (licence)
• Geometric Graph Learning with Extended Atom-Types Features for Protein-Ligand Binding Affinity Prediction
  15 Jan 2023 1 repository listed
• Critical review of conformational B-cell epitope prediction methods
  10 Jan 2023 1 repository listed
• SVSBI: Sequence-based virtual screening of biomolecular interactions
  27 Dec 2022 1 repository listed
• Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing
  21 Dec 2022 1 repository listed Syntology official (archive's flag): 1 ran · 2 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 2 unverified (of 4 harvested samples) · 4 pointer-only (licence)
• Protein Language Models and Structure Prediction: Connection and Progression
  30 Nov 2022 1 repository listed
• Reinforced Genetic Algorithm for Structure-based Drug Design
  28 Nov 2022 1 repository listed
• An Efficient MCMC Approach to Energy Function Optimization in Protein Structure Prediction
  6 Nov 2022 1 repository listed
• Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design
  6 Oct 2022 1 repository listed Syntology official (archive's flag): 4 ran · 4 ran (of which 0 constructed an object rather than computing a result; 2 with no instrument failure: 0 honoured, 0 violated, 2 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified (of 4 harvested samples)
• Uni-Mol: A Universal 3D Molecular Representation Learning Framework
  8 Sep 2022 1 repository listed
• Exploiting Pretrained Biochemical Language Models for Targeted Drug Design
  2 Sep 2022 1 repository listed
• HiGNN: Hierarchical Informative Graph Neural Networks for Molecular Property Prediction Equipped with Feature-Wise Attention
  30 Aug 2022 1 repository listed
• Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design
  30 Aug 2022 1 repository listed Syntology official (archive's flag): 3 ran · 3 ran (of which 0 constructed an object rather than computing a result; 3 with no instrument failure: 0 honoured, 0 violated, 3 with no contract checked; 0 where Syntology's instrument failed) · 2 unverified (of 5 harvested samples) · 5 pointer-only (licence)
• From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning
  19 Aug 2022 1 repository listed
• A fully differentiable ligand pose optimization framework guided by deep learning and traditional scoring functions
  27 Jun 2022 1 repository listed
• 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design
  15 May 2022 1 repository listed
• Insights into performance evaluation of com-pound-protein interaction prediction methods
  28 Jan 2022 1 repository listed
• Molecular Contrastive Learning with Chemical Element Knowledge Graph
  1 Dec 2021 1 repository listed Syntology official (archive's flag): 2 ran · 2 ran (of which 0 constructed an object rather than computing a result; 2 with no instrument failure: 0 honoured, 0 violated, 2 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified (of 3 harvested samples)
• Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking
  15 Nov 2021 1 repository listed Syntology official (archive's flag): 3 ran · 3 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 3 where Syntology's instrument failed) · 0 unverified (of 3 harvested samples)
• Equivalent Distance Geometry Error for Molecular Conformation Comparison
  13 Nov 2021 1 repository listed
• Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spaces
  1 Nov 2021 1 repository listed Syntology official (archive's flag): 2 ran · 2 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified (of 2 harvested samples) · 2 pointer-only (licence)
• DOCKSTRING: easy molecular docking yields better benchmarks for ligand design
  29 Oct 2021 1 repository listed
• GraphGT: Machine Learning Datasets for Graph Generation and Transformation
  24 Sep 2021 1 repository listed
• Improving black-box optimization in VAE latent space using decoder uncertainty
  30 Jun 2021 1 repository listed Syntology 6 ran (of which 0 constructed an object rather than computing a result; 6 with no instrument failure: 0 honoured, 0 violated, 6 with no contract checked; 0 where Syntology's instrument failed) · 2 unverified (of 8 harvested samples)
• Scientific Language Models for Biomedical Knowledge Base Completion: An Empirical Study
  17 Jun 2021 1 repository listed
• Artificial Intelligence in Drug Discovery: Applications and Techniques
  9 Jun 2021 1 repository listed
• Evening the Score: Targeting SARS-CoV-2 Protease Inhibition in Graph Generative Models for Therapeutic Candidates
  7 May 2021 1 repository listed
• Using Molecular Embeddings in QSAR Modeling: Does it Make a Difference?
  20 Mar 2021 1 repository listed
• Molecular Representation Learning by Leveraging Chemical Information
  15 Mar 2021 1 repository listed
• Assigning Confidence to Molecular Property Prediction
  23 Feb 2021 1 repository listed
• Peptipedia: a comprehensive database for peptide research supported by Assembled predictive models and Data Mining approaches
  28 Jan 2021 1 repository listed
• A Comparative Analysis of the Ensemble Methods for Drug Design
  11 Dec 2020 1 repository listed
• Dr-COVID: Graph Neural Networks for SARS-CoV-2 Drug Repurposing
  3 Dec 2020 1 repository listed
• Ollivier persistent Ricci curvature (OPRC) based molecular representation for drug design
  20 Nov 2020 1 repository listed
• Investigating 3D Atomic Environments for Enhanced QSAR
  24 Oct 2020 1 repository listed
• Multiscale Simulations of Complex Systems by Learning their Effective Dynamics
  24 Jun 2020 1 repository listed
• We Should at Least Be Able to Design Molecules That Dock Well
  20 Jun 2020 1 repository listed Syntology official (archive's flag): 8 ran · 8 ran (of which 0 constructed an object rather than computing a result; 8 with no instrument failure: 0 honoured, 0 violated, 8 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified (of 9 harvested samples)
• A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories
  19 Jun 2020 1 repository listed
• Sample-Efficient Optimization in the Latent Space of Deep Generative Models via Weighted Retraining
  16 Jun 2020 1 repository listed Syntology official (archive's flag): 1 ran · 3 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 0 honoured, 0 violated, 1 with no contract checked; 2 where Syntology's instrument failed) · 3 unverified (of 6 harvested samples) · 4 pointer-only (licence)
• Drug–target affinity prediction using graph neural network and contact maps
  1 Jun 2020 1 repository listed
• Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning
  26 Apr 2020 1 repository listed
• A Deep Generative Model for Fragment-Based Molecule Generation
  28 Feb 2020 1 repository listed
• DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction
  1 Dec 2019 1 repository listed
• Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders
  25 Apr 2019 1 repository listed
• N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules
  24 Jun 2018 1 repository listed Syntology official (archive's flag): 5 ran · 5 ran (of which 0 constructed an object rather than computing a result; 5 with no instrument failure: 0 honoured, 0 violated, 5 with no contract checked; 0 where Syntology's instrument failed) · 9 unverified (of 14 harvested samples)
• Sever: A Robust Meta-Algorithm for Stochastic Optimization
  7 Mar 2018 1 repository listed
• Visualizing Convolutional Neural Network Protein-Ligand Scoring
  6 Mar 2018 1 repository listed
• Multi-Objective De Novo Drug Design with Conditional Graph Generative Model
  18 Jan 2018 1 repository listed
• Deep Reinforcement Learning for De-Novo Drug Design
  29 Nov 2017 1 repository listed
• DeeperBind: Enhancing Prediction of Sequence Specificities of DNA Binding Proteins
  17 Nov 2016 1 repository listed
• Discriminative Embeddings of Latent Variable Models for Structured Data
  17 Mar 2016 1 repository listed
• Diverse Mini-Batch Selection in Reinforcement Learning for Efficient Chemical Exploration in de novo Drug Design
  26 Jun 2025 0 repositories listed
• Active Learning-Guided Seq2Seq Variational Autoencoder for Multi-target Inhibitor Generation
  18 Jun 2025 0 repositories listed
• Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion
  17 Jun 2025 0 repositories listed
• A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly
  27 May 2025 0 repositories listed
• Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations
  27 May 2025 0 repositories listed
• Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimization
  22 May 2025 0 repositories listed
• Evolutionary training-free guidance in diffusion model for 3D multi-objective molecular generation
  16 May 2025 0 repositories listed
• Pharmacophore-Conditioned Diffusion Model for Ligand-Based De Novo Drug Design
  15 May 2025 0 repositories listed
• A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization
  9 May 2025 0 repositories listed
• Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning
  5 May 2025 0 repositories listed Syntology 0 ran · 1 unverified (of 1 harvested sample)
• Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks
  1 May 2025 0 repositories listed
• Combining GCN Structural Learning with LLM Chemical Knowledge for or Enhanced Virtual Screening
  24 Apr 2025 0 repositories listed
• Synergistic Benefits of Joint Molecule Generation and Property Prediction
  23 Apr 2025 0 repositories listed
• How to Detect and Defeat Molecular Mirage: A Metric-Driven Benchmark for Hallucination in LLM-based Molecular Comprehension
  10 Apr 2025 0 repositories listed
• Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives
  4 Apr 2025 0 repositories listed
• HCAF-DTA: drug-target binding affinity prediction with cross-attention fused hypergraph neural networks
  2 Apr 2025 0 repositories listed
• TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design
  26 Mar 2025 0 repositories listed
• Two for the Price of One: Integrating Large Language Models to Learn Biophysical Interactions
  26 Mar 2025 0 repositories listed
• Extracting Interpretable Logic Rules from Graph Neural Networks
  25 Mar 2025 0 repositories listed Syntology 6 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 6 where Syntology's instrument failed) · 1 unverified (of 7 harvested samples) · 7 pointer-only (licence)
• Linear to Neural Networks Regression: QSPR of Drugs via Degree-Distance Indices
  18 Mar 2025 0 repositories listed

Syntology lines on 23 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; each line links to that paper's sample list. Syntology's record for this page has not changed since 2026-09-28, the first build that kept a record date for it; when this build read Syntology's graph is in the build record. For agents: get_harvested_code_for_paper(arxiv_id) lists each paper's samples; how to connect.