FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction | Paper Citation Record

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This paper cites Harder, B.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Harder, B

Reference 1

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This paper cites Ballard, Joshua Bambrick, Sebastian W.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Ballard, Joshua Bambrick, Sebastian W

Reference 2

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This paper cites Building Normalizing Flows with Stochastic Interpolants.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Building Normalizing Flows with Stochastic Interpolants

Reference 3

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This paper cites Stochastic Interpolants: A Unifying Framework for Flows and Diffusions.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Stochastic Interpolants: A Unifying Framework for Flows and Diffusions

Reference 4

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This paper cites Bodkin, Stefan Knapp, and Philip C.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Bodkin, Stefan Knapp, and Philip C

Reference 5

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This paper cites Evaluating the use of absolute binding free energy in fragment optimization.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Evaluating the use of absolute binding free energy in fragment optimization

Reference 6

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This paper cites Guided docking as a data generation approach facilitates structure-based machine learning on kinases.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Guided docking as a data generation approach facilitates structure-based machine learning on kinases

Reference 7

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This paper cites Ballester and John B.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Ballester and John B

Reference 8

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This paper cites Gfn2-xtb---an accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributions.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Gfn2-xtb---an accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributions

Reference 9

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This paper cites Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer

Reference 10

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This paper cites Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A

Reference 11

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This paper cites Absolute binding free energies: A quantitative approach for their calculation.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Absolute binding free energies: A quantitative approach for their calculation

Reference 12

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This paper cites Prolif: a library to encode molecular interactions as fingerprints.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Prolif: a library to encode molecular interactions as fingerprints

Reference 13

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This paper cites Deane, and Garrett M.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Deane, and Garrett M

Reference 14

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This paper cites Morris, and Charlotte M.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Morris, and Charlotte M

Reference 15

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This paper cites Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design

Reference 16

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This paper cites Relative binding free energy calculations in drug discovery: Recent advances and practical considerations.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Relative binding free energy calculations in drug discovery: Recent advances and practical considerations

Reference 17

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Unresolved cited work

Reference 18

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This paper cites Flowr: Flow matching for structure-aware de novo, interaction- and fragment-based ligand generation.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Flowr: Flow matching for structure-aware de novo, interaction- and fragment-based ligand generation

Reference 19

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Unresolved cited work

Reference 20

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This paper cites Davis, Jeremy P.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Davis, Jeremy P

Reference 21

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Sequential monte carlo samplers

Reference 22

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This paper cites Plinder: The protein-ligand interactions dataset and evaluation resource.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Plinder: The protein-ligand interactions dataset and evaluation resource

Reference 23

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This paper cites Tillack, and Stefano Forli.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Tillack, and Stefano Forli

Reference 24

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Robust and efficient implicit solvation model for fast semiempirical methods

Reference 25

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This paper cites Absolute binding free energy calculations improve virtual screening in structure-based drug discovery.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Absolute binding free energy calculations improve virtual screening in structure-based drug discovery

Reference 26

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This paper cites Syntalinker-hybrid: A deep learning approach for target specific drug design.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Syntalinker-hybrid: A deep learning approach for target specific drug design

Reference 27

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This paper cites Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia, Richard B.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia, Richard B

Reference 28

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Friesner et al

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This paper cites Gumbart, Fran c ois Dehez, Beno \^i t Roux, Wensheng Cai, and Christophe Chipot.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Gumbart, Fran c ois Dehez, Beno \^i t Roux, Wensheng Cai, and Christophe Chipot

Reference 30

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules

Reference 31

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction u ller, and Kristof T. Sch \

Reference 32

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Autoregressive fragment-based diffusion for pocket-aware ligand design

Reference 33

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Gilson and Huan-Xiang Zhou

Reference 34

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Gilson, James A

Reference 35

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Unresolved cited work

Reference 36

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This paper cites Popowicz, Oliver Plettenburg, Grzegorz Dubin, Filipe Menezes, and Anna Czarna.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Popowicz, Oliver Plettenburg, Grzegorz Dubin, Filipe Menezes, and Anna Czarna

Reference 37

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction 3d equivariant diffusion for target-aware molecule generation and affinity prediction

Reference 38

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Link-invent: generative linker design with reinforcement learning

Reference 39

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Hadfield et al

Reference 40

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Denoising diffusion probabilistic models

Reference 41

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Denoising Diffusion Probabilistic Models

Reference 42

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Free energy calculations by the molecular mechanics poisson–boltzmann surface area method

Reference 43

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Equivariant diffusion for molecule generation in 3 D

Reference 44

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This paper cites Benson, Randy D.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Benson, Randy D

Reference 45

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This paper cites Equivariant 3d-conditional diffusion model for molecular linker design.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Equivariant 3d-conditional diffusion model for molecular linker design

Reference 46

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Deep generative models for 3d linker design

Reference 47

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This paper cites Irwin, Khanh G.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Irwin, Khanh G

Reference 48

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matching

Reference 49

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

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Interactiongraphnet: A novel and efficient deep graph representation learning framework for accurate protein--ligand interaction predictions

Reference 50

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This paper cites k\_ DEEP : Protein–ligand absolute binding affinity prediction via 3d-convolutional neural networks.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction k\_ DEEP : Protein–ligand absolute binding affinity prediction via 3d-convolutional neural networks

Reference 51

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This paper cites Torsional Diffusion for Molecular Conformer Generation.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Torsional Diffusion for Molecular Conformer Generation

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This paper cites Johnston, Kun Yao, Zachary Kaplan, Monica Chelliah, Karl Leswing, Sean Seekins, Shawn Watts, David Calkins, Jackson Chief Elk, Steven V.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Johnston, Kun Yao, Zachary Kaplan, Monica Chelliah, Karl Leswing, Sean Seekins, Shawn Watts, David Calkins, Jackson Chief Elk, Steven V

Reference 53

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This paper cites Development and validation of a genetic algorithm for flexible docking.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Development and validation of a genetic algorithm for flexible docking

Reference 54

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Jorgensen

Reference 55

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Karlov, Sergey Sosnin, Maxim V

Reference 56

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Inference-time scaling for flow models via stochastic generation and rollover budget forcing, 2025

Reference 57

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Variational diffusion models

Reference 58

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Reference 59

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This paper cites A machine learning approach towards the prediction of protein--ligand binding affinity based on fundamental molecular properties.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction A machine learning approach towards the prediction of protein--ligand binding affinity based on fundamental molecular properties

Reference 60

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Navigating the design space of equivariant diffusion-based generative models for de novo 3d molecule generation, 2023

Reference 61

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Structural basis for the selective inhibition of Cdc2-Like kinases by CX-4945

Reference 62

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Fragfm: Efficient fragment-based molecular generation via discrete flow matching

Reference 63

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Shields, Thomas Merth, Punit K

Reference 64

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Levine, Muhammed Shuaibi, Evan Walter Clark Spotte-Smith, Michael G

Reference 65

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Structure-aware interactive graph neural networks for the prediction of protein–ligand binding affinity

Reference 66

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction A high-quality data set of protein--ligand binding interactions via comparative complex structure modeling

Reference 67

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This paper cites Assessing protein--ligand interaction scoring functions with the casf-2013 benchmark.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Assessing protein--ligand interaction scoring functions with the casf-2013 benchmark

Reference 68

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Flow Matching for Generative Modeling

Reference 69

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Classification of current scoring functions

Reference 70

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow

Reference 71

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction An autoregressive flow model for 3d molecular geometry generation from scratch

Reference 72

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Inference-Time Scaling for Diffusion Models beyond Scaling Denoising Steps

Reference 73

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Manning, D

Reference 74

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Morris, and Philip C

Reference 75

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Popowicz

Reference 76

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Unresolved cited work

Reference 77

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Mobley and Pavel V

Reference 78

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Accurate protein--ligand binding free energy estimation using qm/mm and the mining minima method

Reference 79

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Quinn, Trung Nguyen, and Svetha Venkatesh

Reference 80

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction O'Boyle, Michael Banck, Craig A

Reference 81

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction O zt \"u rk, Arzucan \

Reference 82

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Review and analysis of synthetic dataset generation methods and techniques for application in computer vision

Reference 83

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Sqm2.20: Semiempirical quantum-mechanical scoring function yields dft-quality protein--ligand binding affinity predictions in minutes

Reference 84

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Data augmentation techniques in natural language processing

Reference 85

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Blum, and Lars Ruddigkeit

Reference 86

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Biggin, and Aniket Magarkar

Reference 87

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction High-Resolution Image Synthesis with Latent Diffusion Models

Reference 88

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Ross, Chao Lu, Guido Scarabelli, and Lingle Wang

Reference 90

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, and Woody Sherman

Reference 91

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Hadfield, Oliver M

Reference 92

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Observation fd82c09a-749b-49ca-9b29-9bf46ca531cb · outbound

This paper cites Structure-based Drug Design with Equivariant Diffusion Models.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Structure-based Drug Design with Equivariant Diffusion Models

Reference 93

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Dobbelstein, Thomas Castiglione, Michael M

Reference 94

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Equivariant message passing for the prediction of tensorial properties and molecular spectra

Reference 95

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This paper cites Rewarding Progress: Scaling Automated Process Verifiers for LLM Reasoning.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Rewarding Progress: Scaling Automated Process Verifiers for LLM Reasoning

Reference 96

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction A general framework for inference-time scaling and steering of diffusion models

Reference 97

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Scaling LLM Test-Time Compute Optimally can be More Effective than Scaling Model Parameters

Reference 98

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Deep unsupervised learning using nonequilibrium thermodynamics

Reference 99

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FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Score-Based Generative Modeling through Stochastic Differential Equations

Reference 101

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This paper cites Clark Still, Anna Tempczyk, Ronald C.

FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction Clark Still, Anna Tempczyk, Ronald C

Reference 102

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