Molecular Docking

Description from the archive archive 2025-07-28; Papers-with-Code links inside it are rewritten to this site.

Benchmarks archive 2025-07-28

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Datasets archive 2025-07-28

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Subtasks archive 2025-07-28

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Most implemented papers archive 2025-07-28

30 shown of 38 papers with code (128 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.

• 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.
• 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.
• Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity
  30 Mar 2017 3 repositories listed Syntology ran 2 of 2 samples · 0 unverified · 2 pointer-only (licence)
  The atomic convolutional neural network is trained to predict the experimentally determined binding affinity of a protein-ligand complex by direct calculation of the energy associated with the complex, protein, and…
• Fast and Accurate Blind Flexible Docking
  20 Feb 2025 2 repositories listed Syntology ran 3 of 4 samples · 1 unverified
  Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery.
• CompassDock: Comprehensive Accurate Assessment Approach for Deep Learning-Based Molecular Docking in Inference and Fine-Tuning
  10 Jun 2024 2 repositories listed
  Our results show that, while fine-tuning without Compass improves the percentage of docked poses with RMSD < 2{\AA}, it leads to a decrease in physical/chemical and bioactivity favorability.
• 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.
• CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions
  26 Jun 2025 1 repository listed
  Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are…
• PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning
  24 Jun 2025 1 repository listed
  Sampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets.
• PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking
  3 May 2025 1 repository listed Syntology ran 0 of 5 samples · 5 unverified
  Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications.
• Scaling Structure Aware Virtual Screening to Billions of Molecules with SPRINT
  23 Nov 2024 1 repository listed
  Virtual screening of small molecules against protein targets can accelerate drug discovery and development by predicting drug-target interactions (DTIs).
• QuickBind: A Light-Weight And Interpretable Molecular Docking Model
  21 Oct 2024 1 repository listed
  For high-throughput virtual screening applications, this exposes a capability gap that can be filled by moderately accurate but fast pose prediction.
• MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning
  15 Oct 2024 1 repository listed Syntology ran 3 of 9 samples · 6 unverified · 3 pointer-only (licence)
  More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model.
• DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking
  15 Oct 2024 1 repository listed
  Despite these advancements, current methods are often tailored for specific docking settings, and limitations such as the neglect of protein side-chain structures, difficulties in handling large binding pockets, and…
• DisCo-Diff: Enhancing Continuous Diffusion Models with Discrete Latents
  3 Jul 2024 1 repository listed Syntology ran 6 of 6 samples · 0 unverified
  The discrete latents significantly simplify learning the DM's complex noise-to-data mapping by reducing the curvature of the DM's generative ODE.
• Understanding active learning of molecular docking and its applications
  14 Jun 2024 1 repository listed
  With the advancing capabilities of computational methodologies and resources, ultra-large-scale virtual screening via molecular docking has emerged as a prominent strategy for in silico hit discovery.
• Smiles2Dock: an open large-scale multi-task dataset for ML-based molecular docking
  9 Jun 2024 1 repository listed
  We also introduce a novel Transformer-based architecture for docking scores prediction and set it as an initial benchmark for our dataset.
• Screening of BindingDB database ligands against EGFR, HER2, Estrogen, Progesterone and NF-kB receptors based on machine learning and molecular docking
  1 May 2024 1 repository listed
  This dendrogram aims to facilitate the exploration of chemical space for various therapeutic targets.
• Protein language models are performant in structure-free virtual screening
  20 Apr 2024 1 repository listed
  Hitherto virtual screening has been typically performed using a structure-based drug design paradigm.
• FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation
  29 Mar 2024 1 repository listed
  Molecular docking is a pivotal process in drug discovery.
• DeepRLI: A Multi-objective Framework for Universal Protein--Ligand Interaction Prediction
  19 Jan 2024 1 repository listed
  In order to equip the model to generalize to conformations beyond the confines of crystal structures and to adapt to molecular docking and virtual screening tasks, we propose a multi-objective strategy, that is, the…
• FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction
  18 Jan 2024 1 repository listed Syntology ran 8 of 9 samples · 1 unverified
  A rational design of new therapeutic drugs aims to find a molecular structure with desired biological functionality, e.
• Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms
  7 Dec 2023 1 repository listed Syntology ran 2 of 4 samples · 2 unverified
  The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket.
• Enhancing Ligand Pose Sampling for Molecular Docking
  30 Nov 2023 1 repository listed Syntology ran 1 of 3 samples · 2 unverified
  To train scoring functions-and to perform molecular docking-one must generate a set of candidate ligand binding poses.
• DiffBindFR: An SE(3) Equivariant Network for Flexible Protein-Ligand Docking
  26 Nov 2023 1 repository listed Syntology ran 13 of 15 samples · 2 unverified · 15 pointer-only (licence)
  Furthermore, in the Apo and AlphaFold2 modeled structures, DiffBindFR demonstrates superior advantages in accurate ligand binding pose and protein binding conformation prediction, making it suitable for Apo and…
• PLANTAIN: Diffusion-inspired Pose Score Minimization for Fast and Accurate Molecular Docking
  22 Jul 2023 1 repository listed Syntology ran 6 of 7 samples · 1 unverified
  Traditional docking methods predict ligand poses by minimizing a physics-inspired scoring function.
• Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats
  17 Jul 2023 1 repository listed
  With this dataset, we trained graph neural fingerprint docking models for high-throughput virtual COVID-19 drug screening.
• Optimization of binding affinities in chemical space with generative pretrained transformer and deep reinforcement learning
  3 Apr 2023 1 repository listed
  The SGPT-RL method achieved better results than Reinvent on the ACE2 task, where molecular docking was used as the optimization goal.
• Modeling Molecular Structures with Intrinsic Diffusion Models
  23 Feb 2023 1 repository listed
  Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take…
• Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction
  4 Feb 2023 1 repository listed
  However, many important molecular properties depend on complex molecular characteristics -- such as the various 3D geometries a molecule may adopt or the types of chemical interactions it can form -- that are not…
• Domain-Agnostic Molecular Generation with Chemical Feedback
  26 Jan 2023 1 repository listed Syntology ran 3 of 5 samples · 2 unverified
  The generation of molecules with desired properties has become increasingly popular, revolutionizing the way scientists design molecular structures and providing valuable support for chemical and drug design.

Syntology lines on 14 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.