DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction | Paper Citation Record

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This paper cites Berman, John Westbrook, Zukang Feng, Gary Gilliland, T.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Berman, John Westbrook, Zukang Feng, Gary Gilliland, T

Reference 1

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Observation c4c5d9bb-9802-4104-a8c6-81c0839f11ad · outbound

This paper cites A simple framework for contrastive learning of visual representations.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction A simple framework for contrastive learning of visual representations

Reference 2

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This paper cites Comprehensive analysis of kinase inhibitor selectivity.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Comprehensive analysis of kinase inhibitor selectivity

Reference 3

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This paper cites Autodock vina 1.2.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Autodock vina 1.2

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:15.247484Z

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This paper cites Knowledge graph-enhanced molecular contrastive learning with functional prompt.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Knowledge graph-enhanced molecular contrastive learning with functional prompt

Reference 5

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Observation bfabbea3-5cdd-418f-9c73-a7d05e831679 · outbound

This paper cites Potentialnet for molecular property prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Potentialnet for molecular property prediction

Reference 6

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This paper cites Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design

Reference 7

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Observation edfe20fe-e390-46a6-bcfc-03212d17a4f7 · outbound

This paper cites The mm/pbsa and mm/gbsa methods to estimate ligand-binding affinities.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction The mm/pbsa and mm/gbsa methods to estimate ligand-binding affinities

Reference 8

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Observation 90ba7aea-0fad-43c2-8389-c19aa8c39a0e · outbound

This paper cites T-mgcl: Molecule graph contrastive learning based on transformer for molecular property prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction T-mgcl: Molecule graph contrastive learning based on transformer for molecular property prediction

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:15.163624Z

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This paper cites Momentum contrast for unsupervised visual representation learning.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Momentum contrast for unsupervised visual representation learning

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:15.149336Z

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This paper cites Masked autoencoders are scalable vision learners.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Masked autoencoders are scalable vision learners

Reference 11

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Observation ebafe3d4-fa80-43c0-a8a5-d04a08556394 · outbound

This paper cites Interactiongraphnet: A novel and efficient deep graph representation learning framework for accurate protein–ligand interaction predictions.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Interactiongraphnet: A novel and efficient deep graph representation learning framework for accurate protein–ligand interaction predictions

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:15.122853Z

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Observation 45728999-ba28-49be-a686-d3b72379eb48 · outbound

This paper cites Unsupervised protein-ligand binding energy prediction via neural euler's rotation equation.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Unsupervised protein-ligand binding energy prediction via neural euler's rotation equation

Reference 13

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This paper cites Statistical mechanics of fluid mixtures.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Statistical mechanics of fluid mixtures

Reference 14

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This paper cites Docking and scoring in virtual screening for drug discovery: methods and applications.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Docking and scoring in virtual screening for drug discovery: methods and applications

Reference 15

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This paper cites Modelling drug-target binding affinity using a bert based graph neural network.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Modelling drug-target binding affinity using a bert based graph neural network

Reference 16

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DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Unresolved cited work

Reference 17

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Observation ab6ac7e6-a605-4c2f-914b-17176f8bd764 · outbound

This paper cites Machine-learning scoring functions for structure-based drug lead optimization.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Machine-learning scoring functions for structure-based drug lead optimization

Reference 18

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This paper cites Geomgcl: Geometric graph contrastive learning for molecular property prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Geomgcl: Geometric graph contrastive learning for molecular property prediction

Reference 19

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This paper cites Dyscore: A boosting scoring method with dynamic properties for identifying true binders and nonbinders in structure-based drug discovery.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Dyscore: A boosting scoring method with dynamic properties for identifying true binders and nonbinders in structure-based drug discovery

Reference 20

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Observation 69aca9f5-c447-4be7-878a-a0e52a0d3c44 · outbound

This paper cites Leak proof pdbbind: a reorganized dataset of protein-ligand complexes for more generalizable binding affinity prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Leak proof pdbbind: a reorganized dataset of protein-ligand complexes for more generalizable binding affinity prediction

Reference 21

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Observation 6e9ab14a-be22-4fa0-bf10-a47b0cc993fb · outbound

This paper cites A high-quality data set of protein--ligand binding interactions via comparative complex structure modeling.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction A high-quality data set of protein--ligand binding interactions via comparative complex structure modeling

Reference 22

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Observation e6b93d48-1b14-4118-88e5-7885067d788e · outbound

This paper cites Predicting drug–target interaction using a novel graph neural network with 3d structure-embedded graph representation.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Predicting drug–target interaction using a novel graph neural network with 3d structure-embedded graph representation

Reference 23

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Observation a765b253-91b2-46ff-a27b-5ef9bc29f157 · outbound

This paper cites Bindingdb: a web-accessible database of experimentally determined protein--ligand binding affinities.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Bindingdb: a web-accessible database of experimentally determined protein--ligand binding affinities

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.946048Z

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This paper cites Hiermrl: Hierarchical structure-aware molecular representation learning for property prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Hiermrl: Hierarchical structure-aware molecular representation learning for property prediction

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.932264Z

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This paper cites Graphprompt: Unifying pre-training and downstream tasks for graph neural networks.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Graphprompt: Unifying pre-training and downstream tasks for graph neural networks

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.917622Z

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This paper cites Enhancing generalizability in protein--ligand binding affinity prediction with multimodal contrastive learning.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Enhancing generalizability in protein--ligand binding affinity prediction with multimodal contrastive learning

Reference 27

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This paper cites Dockingapp rf: a state-of-the-art novel scoring function for molecular docking in a user-friendly interface to autodock vina.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Dockingapp rf: a state-of-the-art novel scoring function for molecular docking in a user-friendly interface to autodock vina

Reference 28

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This paper cites Pubchemqc project: a large-scale first-principles electronic structure database for data-driven chemistry.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Pubchemqc project: a large-scale first-principles electronic structure database for data-driven chemistry

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.873173Z

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Observation 9a504678-d615-492d-8853-941464bf2988 · outbound

This paper cites GraphDTA: predicting drug–target binding affinity with graph neural networks.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction GraphDTA: predicting drug–target binding affinity with graph neural networks

Reference 30

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Observation b989ecc0-97ed-458c-96a1-b88c47303eab · outbound

This paper cites Pre-training with fractional denoising to enhance molecular property prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Pre-training with fractional denoising to enhance molecular property prediction

Reference 31

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Observation 7bdc7860-b413-4f17-8ad1-fa2899cf8ee6 · outbound

This paper cites A probability contrastive learning framework for 3d molecular representation learning.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction A probability contrastive learning framework for 3d molecular representation learning

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.827827Z

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Observation 2bb3c758-6250-451b-9acb-14ee8e5a9c57 · outbound

This paper cites Improving language understanding by generative pre-training.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Improving language understanding by generative pre-training

Reference 33

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This paper cites Deep learning in drug design: Protein-ligand binding affinity prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Deep learning in drug design: Protein-ligand binding affinity prediction

Reference 34

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Observation e0cf8933-1c34-4b32-8f17-ecc77b70821a · outbound

This paper cites E (n) equivariant graph neural networks.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction E (n) equivariant graph neural networks

Reference 35

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This paper cites u tt, Pieter-Jan Kindermans, Huziel Enoc Sauceda Felix, Stefan Chmiela, Alexandre Tkatchenko, and Klaus-Robert M\.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction u tt, Pieter-Jan Kindermans, Huziel Enoc Sauceda Felix, Stefan Chmiela, Alexandre Tkatchenko, and Klaus-Robert M\

Reference 36

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.775664Z

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This paper cites Misato: machine learning dataset of protein--ligand complexes for structure-based drug discovery.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Misato: machine learning dataset of protein--ligand complexes for structure-based drug discovery

Reference 37

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Observation 53cdf5fc-162a-46dd-b758-05e326b2cb96 · outbound

This paper cites Development and evaluation of a deep learning model for protein--ligand binding affinity prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Development and evaluation of a deep learning model for protein--ligand binding affinity prediction

Reference 38

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Observation 565d28f9-e9a1-45a9-80d5-fef6fdff28ef · outbound

This paper cites Development and evaluation of a deep learning model for protein–ligand binding affinity prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.733428Z

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Observation 94c36f0e-9ae9-497c-85d4-7ac230366205 · outbound

This paper cites Mocl: data-driven molecular fingerprint via knowledge-aware contrastive learning from molecular graph.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Mocl: data-driven molecular fingerprint via knowledge-aware contrastive learning from molecular graph

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.720419Z

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Observation 5aeec1ff-56f9-4645-8fdd-827463c56567 · outbound

This paper cites Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis

Reference 41

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.705933Z

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Observation 6c26d2ef-bc90-4eb2-b56d-1dd7c57dbc34 · outbound

This paper cites Equivariant transformers for neural network based molecular potentials.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Equivariant transformers for neural network based molecular potentials

Reference 42

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.691640Z

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Observation f4695b4b-0660-4c0d-bb09-6deec5d6371a · outbound

This paper cites Directed graph contrastive learning.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Directed graph contrastive learning

Reference 43

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.676899Z

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Observation dfd2551b-b1eb-4238-b125-d1d580d524a6 · outbound

This paper cites Sunsetting binding moad with its last data update and the addition of 3d-ligand polypharmacology tools.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Sunsetting binding moad with its last data update and the addition of 3d-ligand polypharmacology tools

Reference 44

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.662890Z

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Observation e4b91788-7074-49e5-9a6a-051a88bb93a9 · outbound

This paper cites Contrastive learning with stronger augmentations.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Contrastive learning with stronger augmentations

Reference 45

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.649176Z

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Observation 5c091ed9-c0d3-4d37-9b5a-4d06b9072d29 · outbound

This paper cites The pdbbind database: methodologies and updates.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction The pdbbind database: methodologies and updates

Reference 46

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.635063Z

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Observation 23008302-704b-494f-9136-6f2c1009bb4d · outbound

This paper cites A workflow to create a high-quality protein--ligand binding dataset for training, validation, and prediction tasks.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction A workflow to create a high-quality protein--ligand binding dataset for training, validation, and prediction tasks

Reference 47

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.619544Z

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Observation db693034-0772-4671-8714-1a2e7c223714 · outbound

This paper cites Pre-training of equivariant graph matching networks with conformation flexibility for drug binding.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Pre-training of equivariant graph matching networks with conformation flexibility for drug binding

Reference 48

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.603241Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 18d523a6-50b5-4ce3-9c2a-b1fe9e5de317 · outbound

This paper cites Infogcl: Information-aware graph contrastive learning.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Infogcl: Information-aware graph contrastive learning

Reference 49

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.586984Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 4710117a-b740-4b7e-ad96-b23781e15dfc · outbound

This paper cites Biolip: a semi-manually curated database for biologically relevant ligand--protein interactions.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Biolip: a semi-manually curated database for biologically relevant ligand--protein interactions

Reference 50

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.570984Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation a89a4f0a-37a2-42a5-9dc7-d84bb85384ac · outbound

This paper cites Geometric interaction graph neural network for predicting protein--ligand binding affinities from 3d structures (gign).

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Geometric interaction graph neural network for predicting protein--ligand binding affinities from 3d structures (gign)

Reference 51

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.555631Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 2816c22c-af7d-4fb5-90d0-e8ac982686b3 · outbound

This paper cites Graph contrastive learning with augmentations.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Graph contrastive learning with augmentations

Reference 52

Resolution: unresolved; no resolver link, observed 2026-08-06T19:13:14.405171Z

Source-reported events for the cited work

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Observation 222be547-8622-4cf0-880e-81aad6f1269b · outbound

This paper cites Pre-training via denoising for molecular property prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Pre-training via denoising for molecular property prediction

Reference 53

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.527707Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 4f265b41-148f-4417-8d03-4dcfd9ca5120 · outbound

This paper cites Machine learning for sequence and structure-based protein--ligand interaction prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Machine learning for sequence and structure-based protein--ligand interaction prediction

Reference 54

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.511235Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 244c3b71-34ed-46cb-b723-2417ab8955d7 · outbound

This paper cites Onionnet: a multiple-layer intermolecular-contact-based convolutional neural network for protein--ligand binding affinity prediction.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction Onionnet: a multiple-layer intermolecular-contact-based convolutional neural network for protein--ligand binding affinity prediction

Reference 55

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.494779Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 8958ef80-af96-4ba6-b0f6-6970072684fe · outbound

This paper cites High-temperature equation of state by a perturbation method.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction High-temperature equation of state by a perturbation method

Reference 56

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T19:13:14.479524Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation ca214326-3438-496b-831e-cd9fe8b530a9 · outbound

This paper cites write newline.

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction write newline

Reference 57

Resolution: unresolved; no resolver link, observed 2026-08-06T19:13:14.425176Z

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