Drug Design

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Most implemented papers archive 2025-07-28

30 shown of 180 papers with code (440 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond
  13 Jul 2023 7 repositories listed
  The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation…
• Multi-Objective Molecule Generation using Interpretable Substructures
  8 Feb 2020 5 repositories listed Syntology ran 1 of 3 samples · 2 unverified
  These rationales are identified from molecules as substructures that are likely responsible for each property of interest.
• Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks
  5 Jan 2017 5 repositories listed Syntology ran 0 of 1 samples · 1 unverified
  In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target.
• DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback
  20 Nov 2024 4 repositories listed
  One promising algorithm is DrugGPT, a transformer-based model, that generates small molecules for input protein sequences.
• 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction
  6 Mar 2023 4 repositories listed Syntology ran 3 of 6 samples · 3 unverified · 1 pointer-only (licence)
  Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}.
• Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
  15 May 2022 4 repositories listed Syntology ran 1 of 1 samples · 0 unverified
  Deep generative models have achieved tremendous success in designing novel drug molecules in recent years.
• A 3D Generative Model for Structure-Based Drug Design
  20 Mar 2022 4 repositories listed Syntology ran 4 of 4 samples · 0 unverified
  In this paper, we propose a 3D generative model that generates molecules given a designated 3D protein binding site.
• Generative Flows on Synthetic Pathway for Drug Design
  6 Oct 2024 3 repositories listed Syntology ran 1 of 3 samples · 2 unverified
  This enables RxnFlow to learn generative flows over extensive action spaces comprising combinations of 1.
• Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction
  20 May 2024 3 repositories listed Syntology ran 3 of 3 samples · 0 unverified
  In recent years, machine learning (ML) methods have emerged as promising alternatives for molecular docking, offering the potential for high accuracy without incurring prohibitive computational costs.
• TacoGFN: Target-conditioned GFlowNet for Structure-based Drug Design
  5 Oct 2023 3 repositories listed Syntology ran 6 of 10 samples · 4 unverified · 1 pointer-only (licence)
  We design TacoGFN, a novel GFlowNet-based approach for structure-based drug design, which can generate molecules conditioned on any protein pocket structure with probabilities proportional to its affinity and property…
• SHREC 2022: Protein-ligand binding site recognition
  13 Jun 2022 3 repositories listed Syntology ran 2 of 7 samples · 5 unverified · 4 pointer-only (licence)
  This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition.
• Hopfield Networks is All You Need
  16 Jul 2020 3 repositories listed Syntology ran 0 of 9 samples · 9 unverified
  The new update rule is equivalent to the attention mechanism used in transformers.
• Self-Supervised Graph Transformer on Large-Scale Molecular Data
  18 Jun 2020 3 repositories listed
  We pre-train GROVER with 100 million parameters on 10 million unlabelled molecules -- the biggest GNN and the largest training dataset in molecular representation learning.
• Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations
  9 Nov 2019 3 repositories listed
  Our dataset consists of amino acid sequences, Q8 secondary structures, position specific scoring matrices, multiple sequence alignment co-evolutionary features, backbone atom distance matrices, torsion angles, and 3D…
• Image-Conditioned Graph Generation for Road Network Extraction
  31 Oct 2019 3 repositories listed
  For this, we introduce the Toulouse Road Network dataset, based on real-world publicly-available data.
• Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
  10 Apr 2025 2 repositories listed Syntology ran 0 of 7 samples · 7 unverified
  Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow matching to generate objects in compositional steps while modeling continuous states.
• ACEGEN: Reinforcement learning of generative chemical agents for drug discovery
  7 May 2024 2 repositories listed
  In recent years, reinforcement learning (RL) has emerged as a valuable tool in drug design, offering the potential to propose and optimize molecules with desired properties.
• MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space
  18 Apr 2024 2 repositories listed Syntology ran 8 of 11 samples · 3 unverified · 11 pointer-only (licence)
  Generative models for structure-based drug design (SBDD) have shown promising results in recent years.
• DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design
  26 Feb 2024 2 repositories listed Syntology ran 14 of 19 samples · 5 unverified · 19 pointer-only (licence)
  Designing 3D ligands within a target binding site is a fundamental task in drug discovery.
• De novo Drug Design using Reinforcement Learning with Multiple GPT Agents
  21 Dec 2023 2 repositories listed Syntology ran 3 of 4 samples · 1 unverified · 4 pointer-only (licence)
  A central challenge in this field is to generate molecules with specific properties while also producing a wide range of diverse candidates.
• Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?
  14 Aug 2023 2 repositories listed
  Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years.
• A Systematic Survey of Chemical Pre-trained Models
  29 Oct 2022 2 repositories listed Syntology ran 4 of 5 samples · 1 unverified · 5 pointer-only (licence)
  Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to drug design.
• Structure-based Drug Design with Equivariant Diffusion Models
  24 Oct 2022 2 repositories listed Syntology ran 3 of 8 samples · 5 unverified
  Here we show how a single pre-trained diffusion model can be applied to a broader range of problems, such as off-the-shelf property optimization, explicit negative design, and partial molecular design with inpainting.
• DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
  4 Oct 2022 2 repositories listed Syntology ran 7 of 12 samples · 5 unverified
  We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses.
• Learning programs with magic values
  5 Aug 2022 2 repositories listed
  A magic value in a program is a constant symbol that is essential for the execution of the program but has no clear explanation for its choice.
• Roughness of molecular property landscapes and its impact on modellability
  19 Jul 2022 2 repositories listed Syntology ran 0 of 8 samples · 8 unverified
  In molecular discovery and drug design, structure-property relationships and activity landscapes are often qualitatively or quantitatively analyzed to guide the navigation of chemical space.
• Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders
  23 Mar 2022 2 repositories listed
  Bayesian optimization (BayesOpt) is a gold standard for query-efficient continuous optimization.
• DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks
  10 Aug 2021 2 repositories listed
  A structure-based drug design pipeline involves the development of potential drug molecules or ligands that form stable complexes with a given receptor at its binding site.
• CASTER: Predicting Drug Interactions with Chemical Substructure Representation
  15 Nov 2019 2 repositories listed
  Adverse drug-drug interactions (DDIs) remain a leading cause of morbidity and mortality.
• Fréchet ChemNet Distance: A metric for generative models for molecules in drug discovery
  26 Mar 2018 2 repositories listed Syntology ran 0 of 5 samples · 5 unverified
  We propose a novel distance measure between two sets of molecules, called Fr\'echet ChemNet distance (FCD), that can be used as an evaluation metric for generative models.

Syntology lines on 19 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. Read from the graph 2026-09-24.