Browse State-of-the-Art › Drug Design › Papers, page 3
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 3 of 5: papers 201 to 300 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.
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GenShin:geometry-enhanced structural graph embodies binding pose can better predicting compound-protein interaction affinity16 Mar 2025 0 repositories listed
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Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation8 Mar 2025 0 repositories listed
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Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows6 Mar 2025 0 repositories listed
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Pushing the boundaries of Structure-Based Drug Design through Collaboration with Large Language Models3 Mar 2025 0 repositories listed
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Lattice Protein Folding with Variational Annealing28 Feb 2025 0 repositories listed
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Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold228 Feb 2025 0 repositories listed
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Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks20 Feb 2025 0 repositories listed
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Knowledge-aware contrastive heterogeneous molecular graph learning17 Feb 2025 0 repositories listed
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Towards Efficient Molecular Property Optimization with Graph Energy Based Models17 Feb 2025 0 repositories listed
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E2CB2former: Effecitve and Explainable Transformer for CB2 Receptor Ligand Activity Prediction15 Feb 2025 0 repositories listed
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Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization31 Jan 2025 0 repositories listed
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REINFORCE-ING Chemical Language Models in Drug Design27 Jan 2025 0 repositories listed
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AlgoRxplorers | Precision in Mutation: Enhancing Drug Design with Advanced Protein Stability Prediction Tools13 Jan 2025 0 repositories listed
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Unified Guidance for Geometry-Conditioned Molecular Generation5 Jan 2025 0 repositories listed
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BioTD: an online database of biotoxins28 Dec 2024 0 repositories listed
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Decoding Drug Discovery: Exploring A-to-Z In silico Methods for Beginners15 Dec 2024 0 repositories listed
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Quadratic unconstrained binary optimization and constraint programming approaches for lattice-based cyclic peptide docking13 Dec 2024 0 repositories listed
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Pharmacophore-guided de novo drug design with diffusion bridge10 Dec 2024 0 repositories listed
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Rectified Flow For Structure Based Drug Design2 Dec 2024 0 repositories listed
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Enhancing Molecular Design through Graph-based Topological Reinforcement Learning22 Nov 2024 0 repositories listed
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Hashing for Protein Structure Similarity Search13 Nov 2024 0 repositories listed
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Evaluating Molecule Synthesizability via Retrosynthetic Planning and Reaction Prediction13 Nov 2024 0 repositories listed
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Dockformer: A transformer-based molecular docking paradigm for large-scale virtual screening11 Nov 2024 0 repositories listed
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Improving Molecular Graph Generation with Flow Matching and Optimal Transport8 Nov 2024 0 repositories listed
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SAFE setup for generative molecular design26 Oct 2024 0 repositories listed
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ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design22 Oct 2024 0 repositories listed
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Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development15 Oct 2024 0 repositories listed
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Diversity-Aware Reinforcement Learning for de novo Drug Design14 Oct 2024 0 repositories listed
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Systems-Structure-Based Drug Design14 Oct 2024 0 repositories listed
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Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions12 Oct 2024 0 repositories listed
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SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design3 Oct 2024 0 repositories listed
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Enhancing Solution Efficiency in Reinforcement Learning: Leveraging Sub-GFlowNet and Entropy Integration1 Oct 2024 0 repositories listed
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Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches30 Sep 2024 0 repositories listed
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FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling29 Sep 2024 0 repositories listed
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PepINVENT: Generative peptide design beyond the natural amino acids21 Sep 2024 0 repositories listed
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19 Sep 2024 0 repositories listed
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GFlowNet Pretraining with Inexpensive Rewards15 Sep 2024 0 repositories listed
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Quantum-inspired Reinforcement Learning for Synthesizable Drug Design13 Sep 2024 0 repositories listed
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A Perspective on AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems11 Sep 2024 0 repositories listed
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Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD30 Aug 2024 0 repositories listed
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Quantum-machine-assisted Drug Discovery: Survey and Perspective24 Aug 2024 0 repositories listed
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Mayer-homology learning prediction of protein-ligand binding affinities23 Aug 2024 0 repositories listed
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Genesis: Towards the Automation of Systems Biology Research20 Aug 2024 0 repositories listed
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Fragment and Geometry Aware Tokenization of Molecules for Structure-Based Drug Design Using Language Models19 Aug 2024 0 repositories listed
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GNN-SKAN: Harnessing the Power of SwallowKAN to Advance Molecular Representation Learning with GNNs2 Aug 2024 0 repositories listed
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Vertex-Edge Weighted Molecular Graphs: A study on topological indices and their relevance to physicochemical properties of drugs in use cancer treatment28 Jul 2024 0 repositories listed
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CavDetect: A DBSCAN Algorithm based Novel Cavity Detection Model on Protein Structure25 Jul 2024 0 repositories listed
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Decomposed Direct Preference Optimization for Structure-Based Drug Design19 Jul 2024 0 repositories listed
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Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design15 Jul 2024 0 repositories listed
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Token-Mol 1.0: Tokenized drug design with large language model10 Jul 2024 0 repositories listed
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Leveraging Latent Evolutionary Optimization for Targeted Molecule Generation2 Jul 2024 0 repositories listed
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DCI: An Accurate Quality Assessment Criteria for Protein Complex Structure Models30 Jun 2024 0 repositories listed
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Molecular Diffusion Models with Virtual Receptors26 Jun 2024 0 repositories listed
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A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design24 Jun 2024 0 repositories listed
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Explainable Machine Learning and Deep Learning Models for Predicting TAS2R-Bitter Molecule Interactions21 Jun 2024 0 repositories listed
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Geometric-informed GFlowNets for Structure-Based Drug Design16 Jun 2024 0 repositories listed
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11 Jun 2024 0 repositories listed
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Diffusion Models in De Novo Drug Design7 Jun 2024 0 repositories listed
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Retro-prob: Retrosynthetic Planning Based on a Probabilistic Model25 May 2024 0 repositories listed
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PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance sampling23 May 2024 0 repositories listed
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Improving Targeted Molecule Generation through Language Model Fine-Tuning Via Reinforcement Learning10 May 2024 0 repositories listed
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DrugLLM: Open Large Language Model for Few-shot Molecule Generation7 May 2024 0 repositories listed
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Optimized Drug Design using Multi-Objective Evolutionary Algorithms with SELFIES1 May 2024 0 repositories listed
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Deep Lead Optimization: Leveraging Generative AI for Structural Modification30 Apr 2024 0 repositories listed
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Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design30 Apr 2024 0 repositories listed
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ControlMol: Adding Substructure Control To Molecule Diffusion Models22 Apr 2024 0 repositories listed
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Multi-objective generative AI for designing novel brain-targeting small molecules16 Apr 2024 0 repositories listed
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AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design2 Apr 2024 0 repositories listed
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AlphaFold2 for protein structure prediction: Best practices and critical analyses19 Mar 2024 0 repositories listed
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DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization7 Mar 2024 0 repositories listed
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Stabilizing Policy Gradients for Stochastic Differential Equations via Consistency with Perturbation Process7 Mar 2024 0 repositories listed
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DeepBioisostere: Discovering Bioisosteres with Deep Learning for a Fine Control of Multiple Molecular Properties5 Mar 2024 0 repositories listed
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Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion4 Mar 2024 0 repositories listed
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Exploring Gene Regulatory Interaction Networks and predicting therapeutic molecules for Hypopharyngeal Cancer and EGFR-mutated lung adenocarcinoma27 Feb 2024 0 repositories listed
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Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling22 Feb 2024 0 repositories listed
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Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge18 Feb 2024 0 repositories listed
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Navigating the Maize: Cyclic and conditional computational graphs for molecular simulation22 Jan 2024 0 repositories listed
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Quantum-Inspired Machine Learning for Molecular Docking22 Jan 2024 0 repositories listed
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Deep Manifold Transformation for Protein Representation Learning12 Jan 2024 0 repositories listed
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Cellular forgetting, desensitisation, stress and aging in signalling networks. When do cells refuse to learn more?28 Dec 2023 0 repositories listed
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Hybrid quantum cycle generative adversarial network for small molecule generation28 Dec 2023 0 repositories listed
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PlayMolecule Viewer: a toolkit for the visualization of molecules and other data22 Dec 2023 0 repositories listed
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Automating reward function configuration for drug design15 Dec 2023 0 repositories listed
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From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug Discovery28 Nov 2023 0 repositories listed
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GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks28 Nov 2023 0 repositories listed
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Docking-based generative approaches in the search for new drug candidates22 Nov 2023 0 repositories listed
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Computational Explorations in Biomedicine: Unraveling Molecular Dynamics for Cancer, Drug Delivery, and Biomolecular Insights using LAMMPS Simulations21 Nov 2023 0 repositories listed
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STRIDE: Structure-guided Generation for Inverse Design of Molecules6 Nov 2023 0 repositories listed
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Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods1 Nov 2023 0 repositories listed
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Conformal Drug Property Prediction with Density Estimation under Covariate Shift18 Oct 2023 0 repositories listed
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Docking Peptides into HIV/FIV Protease with Deep Learning and Focused Peptide Docking Methods14 Oct 2023 0 repositories listed
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PointGAT: A quantum chemical property prediction model integrating graph attention and 3D geometry8 Oct 2023 0 repositories listed
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Diffusing on Two Levels and Optimizing for Multiple Properties: A Novel Approach to Generating Molecules with Desirable Properties5 Oct 2023 0 repositories listed
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De Novo Drug Design with Joint Transformers3 Oct 2023 0 repositories listed
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A Comprehensive Review of Generative AI in Healthcare1 Oct 2023 0 repositories listed
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Language models in molecular discovery28 Sep 2023 0 repositories listed
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HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery22 Sep 2023 0 repositories listed
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NLRP3 monomer Functional Dynamics: from the Effects of Allosteric Binding to Implications for Drug Design7 Sep 2023 0 repositories listed
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Unveiling the frontiers of deep learning: innovations shaping diverse domains6 Sep 2023 0 repositories listed
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The known unknowns of the Hsp90 chaperone31 Aug 2023 0 repositories listed