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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 4 of 5: papers 301 to 400 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.

• Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models
  23 Aug 2023 0 repositories listed
• CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations
  25 Jul 2023 0 repositories listed
• Geometric Constraints in Probabilistic Manifolds: A Bridge from Molecular Dynamics to Structured Diffusion Processes
  10 Jul 2023 0 repositories listed
• ReactIE: Enhancing Chemical Reaction Extraction with Weak Supervision
  4 Jul 2023 0 repositories listed
• Meta-Path-based Probabilistic Soft Logic for Drug-Target Interaction Prediction
  25 Jun 2023 0 repositories listed
• SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design
  19 Jun 2023 0 repositories listed
• Happy People -- Image Synthesis as Black-Box Optimization Problem in the Discrete Latent Space of Deep Generative Models
  11 Jun 2023 0 repositories listed
• Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation
  7 Jun 2023 0 repositories listed
• Balancing Exploration and Exploitation: Disentangled β-CVAE in De Novo Drug Design
  2 Jun 2023 0 repositories listed
• Approximation-Generalization Trade-offs under (Approximate) Group Equivariance
  27 May 2023 0 repositories listed
• Generation of 3D Molecules in Pockets via Language Model
  17 May 2023 0 repositories listed
• In Silico Approaches to Deliver Better Antibodies by Design: The Past, the Present and the Future
  12 May 2023 0 repositories listed
• Knowledge graph-enhanced molecular contrastive learning with functional prompt
  4 May 2023 0 repositories listed
• Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks
  4 May 2023 0 repositories listed
• Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text
  30 Mar 2023 0 repositories listed
• Molecular Property Prediction by Semantic-invariant Contrastive Learning
  13 Mar 2023 0 repositories listed
• Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation?
  8 Mar 2023 0 repositories listed
• Accurate Free Energy Estimations of Molecular Systems Via Flow-based Targeted Free Energy Perturbation
  23 Feb 2023 0 repositories listed
• Machine learning for the prediction of safe and biologically active organophosphorus molecules
  21 Feb 2023 0 repositories listed
• Do Deep Learning Models Really Outperform Traditional Approaches in Molecular Docking?
  14 Feb 2023 0 repositories listed
• PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding
  14 Feb 2023 0 repositories listed
• 3D Molecular Generation via Virtual Dynamics
  12 Feb 2023 0 repositories listed
• Transfer Learning for Bayesian Optimization: A Survey
  12 Feb 2023 0 repositories listed
• Protein-protein docking using a tensor train black-box optimization method
  7 Feb 2023 0 repositories listed
• Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy
  5 Feb 2023 0 repositories listed
• Persistent Dirac for molecular representation
  5 Feb 2023 0 repositories listed
• StriderNET: A Graph Reinforcement Learning Approach to Optimize Atomic Structures on Rough Energy Landscapes
  29 Jan 2023 0 repositories listed
• Synthesis-driven design of 3D molecules for structure-based drug discovery using geometric transformers
  31 Dec 2022 0 repositories listed
• EDoG: Adversarial Edge Detection For Graph Neural Networks
  27 Dec 2022 0 repositories listed
• xTrimoABFold: De novo Antibody Structure Prediction without MSA
  30 Nov 2022 0 repositories listed
• Probabilistic thermal stability prediction through sparsity promoting transformer representation
  10 Nov 2022 0 repositories listed
• Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties
  26 Oct 2022 0 repositories listed
• Structure-based drug design with geometric deep learning
  19 Oct 2022 0 repositories listed
• ImmunoLingo: Linguistics-based formalization of the antibody language
  26 Sep 2022 0 repositories listed
• Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model
  14 Aug 2022 0 repositories listed
• Literature Review: Graph Kernels in Chemoinformatics
  9 Aug 2022 0 repositories listed
• A Ligand-and-structure Dual-driven Deep Learning Method for the Discovery of Highly Potent GnRH1R Antagonist to treat Uterine Diseases
  23 Jul 2022 0 repositories listed
• Low cost prediction of probability distributions of molecular properties for early virtual screening
  21 Jul 2022 0 repositories listed
• Prediction of protein allosteric signalling pathways and functional residues through paths of optimised propensity
  14 Jul 2022 0 repositories listed
• Autonomous Drug Design with Multi-Armed Bandits
  4 Jul 2022 0 repositories listed
• LogGENE: A smooth alternative to check loss for Deep Healthcare Inference Tasks
  19 Jun 2022 0 repositories listed
• ScatterSample: Diversified Label Sampling for Data Efficient Graph Neural Network Learning
  9 Jun 2022 0 repositories listed
• One-way Explainability Isn't The Message
  5 May 2022 0 repositories listed
• Molecule Generation for Drug Design: a Graph Learning Perspective
  18 Feb 2022 0 repositories listed
• Interactivity: the missing link between virtual reality technology and drug discovery pipelines
  8 Feb 2022 0 repositories listed
• GENEOnet: A new machine learning paradigm based on Group Equivariant Non-Expansive Operators. An application to protein pocket detection
  31 Jan 2022 0 repositories listed
• Molecule Generation from Input-Attributions over Graph Convolutional Networks
  25 Jan 2022 0 repositories listed
• Semi-Supervised GCN for learning Molecular Structure-Activity Relationships
  25 Jan 2022 0 repositories listed
• AlphaFold Accelerates Artificial Intelligence Powered Drug Discovery: Efficient Discovery of a Novel Cyclin-dependent Kinase 20 (CDK20) Small Molecule Inhibitor
  21 Jan 2022 0 repositories listed
• Reinforcement Learning for Personalized Drug Discovery and Design for Complex Diseases: A Systems Pharmacology Perspective
  21 Jan 2022 0 repositories listed
• Frequent Itemset-driven Search for Finding Minimum Node Separators in Complex Networks
  18 Jan 2022 0 repositories listed
• A Constraint Programming Approach to Weighted Isomorphic Mapping of Fragment-based Shape Signatures
  20 Dec 2021 0 repositories listed
• Learning to Detect Critical Nodes in Sparse Graphs via Feature Importance Awareness
  3 Dec 2021 0 repositories listed
• HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space
  30 Nov 2021 0 repositories listed
• AI challenges for predicting the impact of mutations on protein stability
  8 Nov 2021 0 repositories listed
• Structure-aware generation of drug-like molecules
  7 Nov 2021 0 repositories listed
• De Novo Molecular Generation with Stacked Adversarial Model
  24 Oct 2021 0 repositories listed
• Molecular Graph Generation via Geometric Scattering
  12 Oct 2021 0 repositories listed
• An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design
  10 Oct 2021 0 repositories listed
• Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design
  5 Oct 2021 0 repositories listed
• Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation
  4 Oct 2021 0 repositories listed Syntology 4 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; 1 where Syntology's instrument failed) · 1 unverified (of 5 harvested samples) · 2 pointer-only (licence)
• Pharmacoprint -- a combination of pharmacophore fingerprint and artificial intelligence as a tool for computer-aided drug design
  4 Oct 2021 0 repositories listed
• Knowledge Guided Geometric Editing for Unsupervised Drug Design
  29 Sep 2021 0 repositories listed
• Deep Denerative Models for Drug Design and Response
  14 Sep 2021 0 repositories listed
• Hybrid quantum-classical machine learning for generative chemistry and drug design
  26 Aug 2021 0 repositories listed
• APObind: A Dataset of Ligand Unbound Protein Conformations for Machine Learning Applications in De Novo Drug Design
  23 Aug 2021 0 repositories listed
• New Candidates for Furin Inhibition as Probable Treat for COVID-19: Docking Output
  27 Jul 2021 0 repositories listed
• Machine Learning Implicit Solvation for Molecular Dynamics
  14 Jun 2021 0 repositories listed
• Robust Graph Meta-learning for Weakly-supervised Few-shot Node Classification
  12 Jun 2021 0 repositories listed
• Realistic molecule optimization on a learned graph manifold
  3 Jun 2021 0 repositories listed
• Retro Drug Design: From Target Properties to Molecular Structures
  11 May 2021 0 repositories listed
• tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modeling Structure Refinement
  10 May 2021 0 repositories listed
• Combating small molecule aggregation with machine learning
  1 May 2021 0 repositories listed
• Using the structural kinome to systematize kinase drug discovery
  27 Apr 2021 0 repositories listed
• Learning to design drug-like molecules in three-dimensional space using deep generative models
  17 Apr 2021 0 repositories listed
• ResAtom System: Protein and Ligand Affinity Prediction Model Based on Deep Learning
  17 Apr 2021 0 repositories listed
• Artificial Intelligence based Autonomous Molecular Design for Medical Therapeutic: A Perspective
  10 Feb 2021 0 repositories listed
• ParaVS: A Simple, Fast, Efficient and Flexible Graph Neural Network Framework for Structure-Based Virtual Screening
  8 Feb 2021 0 repositories listed
• Learning to Search for Fast Maximum Common Subgraph Detection
  1 Jan 2021 0 repositories listed
• Calotropin from milk of Calotropis gigantean a potent inhibitor of COVID 19 corona virus infection by Molecular docking studies
  11 Dec 2020 0 repositories listed
• RetroGNN: Approximating Retrosynthesis by Graph Neural Networks for De Novo Drug Design
  25 Nov 2020 0 repositories listed
• Inverted repeats in coronavirus SARS-CoV-2 genome and implications in evolution
  24 Nov 2020 0 repositories listed
• Scaffold-constrained molecular generation
  15 Sep 2020 0 repositories listed
• Surveying the side-chain network approach to protein structure and dynamics: The SARS-CoV-2 spike protein as an illustrative case
  9 Sep 2020 0 repositories listed
• Pre-training of Graph Neural Network for Modeling Effects of Mutations on Protein-Protein Binding Affinity
  28 Aug 2020 0 repositories listed
• Graph-convolution neural network-based flexible docking utilizing coarse-grained distance matrix
  27 Aug 2020 0 repositories listed
• Research and development of MolAICal for drug design via deep learning and classical programming
  17 Jun 2020 0 repositories listed
• InteractionNet: Modeling and Explaining of Noncovalent Protein-Ligand Interactions with Noncovalent Graph Neural Network and Layer-Wise Relevance Propagation
  12 May 2020 0 repositories listed
• Evolutionary Multi-Objective Design of SARS-CoV-2 Protease Inhibitor Candidates
  6 May 2020 0 repositories listed
• Computing Absolute Free Energy with Deep Generative Models
  1 May 2020 0 repositories listed
• Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learning
  29 Apr 2020 0 repositories listed
• Recognition of potential Covid-19 drug treatments through the study of existing protein-drug and protein-protein structures: an analysis of kinetically active residues
  21 Apr 2020 0 repositories listed
• Continuous Representation of Molecules Using Graph Variational Autoencoder
  17 Apr 2020 0 repositories listed
• Molecular docking studies on Jensenone from eucalyptus essential oil as a potential inhibitor of COVID 19 corona virus infection
  17 Apr 2020 0 repositories listed
• CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models
  2 Apr 2020 0 repositories listed
• Application and Assessment of Deep Learning for the Generation of Potential NMDA Receptor Antagonists
  31 Mar 2020 0 repositories listed
• Direct Coupling Analysis of Epistasis in Allosteric Materials
  13 Mar 2020 0 repositories listed
• Old Drugs for Newly Emerging Viral Disease, COVID-19: Bioinformatic Prospective
  10 Mar 2020 0 repositories listed
• Persistent spectral based machine learning (PerSpect ML) for drug design
  3 Feb 2020 0 repositories listed
• Learning of signaling networks: molecular mechanisms
  31 Jan 2020 0 repositories listed

Syntology lines on 1 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.