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ZINC

Introduced in ZINC: A Free Tool to Discover Chemistry for Biology1 Jan 2012 archive 2025-07-28

ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 230 million purchasable compounds in ready-to-dock, 3D formats. ZINC also contains over 750 million purchasable compounds that can be searched for analogs.

Source: ZINC15 Image Source: https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5b00559

HomepageBenchmarksPapers JSON

Benchmarks archive 2025-07-28

All 5 leaderboards whose dataset resolves to this page shown (sort by any header). "First row" is the archive's own first row at snapshot, in the archive's row order; nothing here re-ranks and metric direction is not asserted.

First row (archive order)PaperCode
Graph Regression ZINC-500k ESA + rings + NodeRWSE + EdgeRWSE MAE 0.051 An end-to-end attention-based approach for learning on graphs davidbuterez/edge-set-attention 36 Compare
Graph Regression ZINC ESA + rings + NodeRWSE + EdgeRWSE MAE 0.051 An end-to-end attention-based approach for learning on graphs davidbuterez/edge-set-attention 27 Compare
Graph Regression ZINC-full ESA + rings + NodeRWSE + EdgeRWSE Test MAE 0.0109±0.0002 An end-to-end attention-based approach for learning on graphs davidbuterez/edge-set-attention 19 Compare
Graph Regression ZINC 100k CIN-small MAE 0.094 Weisfeiler and Lehman Go Cellular: CW Networks twitter-research/cwn +1 8 Compare
Graph Ranking ZINC 2-WL-GNN + DirectRanker Kendall's Tau 0.894 Ranking Structured Objects with Graph Neural Networks Cortys/rankgnn 4 Compare

Papers archive 2025-07-28

30 shown of 48 papers with a leaderboard row on this dataset's benchmarks, newest first. The archive's own "papers using this dataset" list was never published, so this is the benchmark-backed subset; the archive's count for this dataset is 251. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.

DateSamples run Syntology
Unlocking the Potential of Classic GNNs for Graph-level Tasks: Simple Architectures Meet Excellence 1 1 13 Feb 2025 ran 4 of 12 samples (8 unverified)
Learning Efficient Positional Encodings with Graph Neural Networks 1 2 3 Feb 2025 not harvested
From Primes to Paths: Enabling Fast Multi-Relational Graph Analysis 1 1 17 Nov 2024 not harvested
Learning Long Range Dependencies on Graphs via Random Walks 1 1 5 Jun 2024 ran 13 of 13 samples (0 unverified)
CKGConv: General Graph Convolution with Continuous Kernels 1 2 21 Apr 2024 ran 8 of 11 samples (3 unverified; 11 pointer-only for licence)
An end-to-end attention-based approach for learning on graphs 1 7 16 Feb 2024 not harvested
Topology-Informed Graph Transformer 2 2 3 Feb 2024 ran 14 of 21 samples (7 unverified; 21 pointer-only for licence)
Graph Transformers without Positional Encodings 0 1 31 Jan 2024 not harvested
Equivariant Matrix Function Neural Networks 0 1 16 Oct 2023 not harvested
Graph-level Representation Learning with Joint-Embedding Predictive Architectures 1 1 27 Sep 2023 ran 10 of 11 samples (1 unverified)
Enhancing Graph Transformers with Hierarchical Distance Structural Encoding 1 1 22 Aug 2023 ran 0 of 1 samples (1 unverified)
Weisfeiler and Lehman Go Paths: Learning Topological Features via Path Complexes 0 1 13 Aug 2023 not harvested
Substructure Aware Graph Neural Networks 1 2 26 Jun 2023 not harvested
CIN++: Enhancing Topological Message Passing 1 3 6 Jun 2023 not harvested
Extending the Design Space of Graph Neural Networks by Rethinking Folklore Weisfeiler-Lehman 1 2 5 Jun 2023 ran 0 of 6 samples (6 unverified)
Graph Inductive Biases in Transformers without Message Passing 2 3 27 May 2023 ran 6 of 12 samples (6 unverified)
Graph Propagation Transformer for Graph Representation Learning 1 1 19 May 2023 ran 4 of 8 samples (4 unverified; 8 pointer-only for licence)
Towards Better Graph Representation Learning with Parameterized Decomposition & Filtering 2 2 10 May 2023 ran 0 of 4 samples (4 unverified)
Self-Attention in Colors: Another Take on Encoding Graph Structure in Transformers 1 2 21 Apr 2023 not harvested
A Generalization of ViT/MLP-Mixer to Graphs 3 1 27 Dec 2022 ran 2 of 3 samples (1 unverified)
Multi-Mask Aggregators for Graph Neural Networks 1 1 24 Nov 2022 not harvested
Pure Transformers are Powerful Graph Learners 2 1 6 Jul 2022 ran 7 of 7 samples (0 unverified; 7 pointer-only for licence)
Automatic Relation-aware Graph Network Proliferation 1 1 31 May 2022 not harvested
Recipe for a General, Powerful, Scalable Graph Transformer 4 4 25 May 2022 ran 3 of 21 samples (18 unverified)
Sign and Basis Invariant Networks for Spectral Graph Representation Learning 2 2 25 Feb 2022 not harvested
A New Perspective on the Effects of Spectrum in Graph Neural Networks 1 1 14 Dec 2021 ran 0 of 2 samples (2 unverified)
Graph Neural Networks with Learnable Structural and Positional Representations 1 3 15 Oct 2021 ran 6 of 7 samples (1 unverified)
Global Self-Attention as a Replacement for Graph Convolution 3 2 7 Aug 2021 ran 0 of 4 samples (4 unverified)
Weisfeiler and Lehman Go Cellular: CW Networks 2 5 23 Jun 2021 not harvested
Do Transformers Really Perform Bad for Graph Representation? 5 2 9 Jun 2021 not harvested

The full list of 48 is in the JSON twin.

Dataset loaders archive 2025-07-28

pytorch-geometric.readthedocs.io/en/latest/modules/datasets.htmlrusty1s/pytorch_geometricpytorch

1 loader as listed in the archive; links are outbound and not re-checked here.

Tasks archive 2025-07-28

Graph RegressionGraph RankingMolecular Graph Generation

License archive 2025-07-28

Custom

Modalities archive 2025-07-28

Interactive

Languages archive 2025-07-28

No language tagged.

Variants archive 2025-07-28

  • ZINC
  • ZINC 100k
  • ZINC-500k
  • ZINC-full

4 variant names, as the archive lists them.

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