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Designing 3D ligands within a target binding site is a fundamental task in drug discovery.
“scaffold-hopping” by topological pharmacophore search: a contribution to virtual screening
Schneider, G., Neidhart, W., Giller, T., and Schmid, G · 1999
Earlier work this paper cites.
The protein data bank
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E · 2000
Earlier work this paper cites.
The process of structure-based drug design
Anderson, A. C · 2003
Earlier work this paper cites.
On the art of compiling and using’drug-like’chemical fragment spaces
Degen, J., Wegscheid-Gerlach, C., Zaliani, A., and Rarey, M · 2008
Earlier work this paper cites.
Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions
Ertl, P. and Schuffenhauer, A · 2009
Earlier work this paper cites.
Open babel: An open chemical toolbox
O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., and Hutchison, G. R · 2011
Earlier work this paper cites.
The practice of medicinal chemistry
Wermuth, C. G · 2011
Earlier work this paper cites.
Quantifying the chemical beauty of drugs
Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S., and Hopkins, A. L · 2012
Earlier work this paper cites.
Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds
Virshup, A. M., Contreras-García, J., Wipf, P., Yang, W., and Beratan, D. N · 2013
Earlier work this paper cites.
Adam: A method for stochastic optimization
Kingma, D. P. and Ba, J · 2014
Earlier work this paper cites.
Alphaspace: fragment-centric topographical mapping to target protein–protein interaction interfaces
Rooklin, D., Wang, C., Katigbak, J., Arora, P. S., and Zhang, Y · 2015
Earlier work this paper cites.
Deep unsupervised learning using nonequilibrium thermodynamics
Sohl-Dickstein, J., Weiss, E., Maheswaranathan, N., and Ganguli, S · 2015
Earlier work this paper cites.
Drugcentral: online drug compendium
Ursu, O., Holmes, J., Knockel, J., Bologa, C. G., Yang, J. J., Mathias, S. L., Nelson, S. J., and Oprea, T. I · 2016
Earlier work this paper cites.
Tensor field networks: Rotation-and translation-equivariant neural networks for 3d point clouds
Thomas, N., Smidt, T., Kearnes, S., Yang, L., Li, L., Kohlhoff, K., and Riley, P · 2018
Earlier work this paper cites.
Deepscaffold: a comprehensive tool for scaffold-based de novo drug discovery using deep learning
Li, Y., Hu, J., Wang, Y., Zhou, J., Zhang, L., and Liu, Z · 2019
Earlier work this paper cites.
Generative modeling by estimating gradients of the data distribution
Song, Y. and Ermon, S · 2019
Earlier work this paper cites.
Analyzing learned molecular representations for property prediction
Yang, K., Swanson, K., Jin, W., Coley, C., Eiden, P., Gao, H., Guzman-Perez, A., Hopper, T., Kelley, B., Mathea, M., et al · 2019
Earlier work this paper cites.
Smiles-based deep generative scaffold decorator for de-novo drug design
Arús-Pous, J., Patronov, A., Bjerrum, E. J., Tyrchan, C., Reymond, J.-L., Chen, H., and Engkvist, O · 2020
Earlier work this paper cites.
Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design
Francoeur, P. G., Masuda, T., Sunseri, J., Jia, A., Iovanisci, R. B., Snyder, I., and Koes, D. R · 2020
Earlier work this paper cites.
Se (3)-transformers: 3d roto-translation equivariant attention networks
Fuchs, F., Worrall, D., Fischer, V., and Welling, M · 2020
Earlier work this paper cites.
Directional message passing for molecular graphs
Gasteiger, J., Groß, J., and Günnemann, S · 2020
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Denoising diffusion probabilistic models
Ho, J., Jain, A., and Abbeel, P · 2020
Cited alongside, same era.
Deep generative models for 3d linker design
Imrie, F., Bradley, A. R., van der Schaar, M., and Deane, C. M · 2020
Cited alongside, same era.
Multi-objective molecule generation using interpretable substructures
Jin, W., Barzilay, R., and Jaakkola, T · 2020
Cited alongside, same era.
Alphaspace 2.0: Representing concave biomolecular surfaces using β \beta -clusters
Katigbak, J., Li, H., Rooklin, D., and Zhang, Y · 2020
Cited alongside, same era.
Scaffold-based molecular design with a graph generative model
Lim, J., Hwang, S.-Y., Moon, S., Kim, S., and Kim, W. Y · 2020
E (n) equivariant graph neural networks
Satorras, V. G., Hoogeboom, E., and Welling, M · 2021
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Fast end-to-end learning on protein surfaces
Sverrisson, F., Feydy, J., Correia, B. E., and Bronstein, M. M · 2021
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Mars: Markov molecular sampling for multi-objective drug discovery
Xie, Y., Shi, C., Zhou, H., Yang, Y., Zhang, W., Yu, Y., and Li, L · 2021
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Knowledge guided geometric editing for unsupervised drug design
Yang, Y., Ouyang, S., Dang, M., Zheng, M., Li, L., and Zhou, H · 2021
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Equivariant shape-conditioned generation of 3d molecules for ligand-based drug design
Adams, K. and Coley, C. W · 2022
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Syntalinker: automatic fragment linking with deep conditional transformer neural networks
Yang, Y., Zheng, S., Su, S., Zhao, C., Xu, J., and Chen, H · 2020
Cited alongside, same era.
Diffusion models beat gans on image synthesis
Dhariwal, P. and Nichol, A · 2021
Cited alongside, same era.
Autodock vina 1.2. 0: New docking methods, expanded force field, and python bindings
Eberhardt, J., Santos-Martins, D., Tillack, A. F., and Forli, S · 2021
Cited alongside, same era.
Independent se (3)-equivariant models for end-to-end rigid protein docking
Ganea, O.-E., Huang, X., Bunne, C., Bian, Y., Barzilay, R., Jaakkola, T., and Krause, A · 2021
Cited alongside, same era.
Argmax flows and multinomial diffusion: Learning categorical distributions
Hoogeboom, E., Nielsen, D., Jaini, P., Forré, P., and Welling, M · 2021
Cited alongside, same era.
Deep generative design with 3d pharmacophoric constraints
Imrie, F., Hadfield, T. E., Bradley, A. R., and Deane, C. M · 2021
Cited alongside, same era.
Guan, J., Qian, W. W., Liu, Q., Ma, W.-Y., Ma, J., and Peng, J · 2022
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Classifier-free diffusion guidance
Ho, J. and Salimans, T · 2022
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Equivariant diffusion for molecule generation in 3d
Hoogeboom, E., Satorras, V. G., Vignac, C., and Welling, M · 2022
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3dlinker: An e (3) equivariant variational autoencoder for molecular linker design
Huang, Y., Peng, X., Ma, J., and Zhang, M · 2022
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Equivariant 3d-conditional diffusion models for molecular linker design
Igashov, I., Stärk, H., Vignac, C., Satorras, V. G., Frossard, P., Welling, M., Bronstein, M., and Correia, B · 2022
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Diffusion-lm improves controllable text generation
Li, X. L., Thickstun, J., Gulrajani, I., Liang, P., and Hashimoto, T. B · 2022
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Diffbp: Generative diffusion of 3d molecules for target protein binding
Lin, H., Huang, Y., Liu, M., Li, X., Ji, S., and Li, S. Z · 2022
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Zero-shot 3d drug design by sketching and generating
Long, S., Zhou, Y., Dai, X., and Zhou, H · 2022
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Pocket2mol: Efficient molecular sampling based on 3d protein pockets
Peng, X., Luo, S., Guan, J., Xie, Q., Peng, J., and Ma, J · 2022
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Hierarchical text-conditional image generation with clip latents
Ramesh, A., Dhariwal, P., Nichol, A., Chu, C., and Chen, M · 2022
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Structure-based drug design with equivariant diffusion models
Schneuing, A., Du, Y., Harris, C., Jamasb, A., Igashov, I., Du, W., Blundell, T., Lió, P., Gomes, C., Welling, M., et al · 2022
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Digress: Discrete denoising diffusion for graph generation
Vignac, C., Krawczuk, I., Siraudin, A., Wang, B., Cevher, V., and Frossard, P · 2022
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Geodiff: A geometric diffusion model for molecular conformation generation
Xu, M., Yu, L., Song, Y., Shi, C., Ermon, S., and Tang, J · 2022
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3d equivariant diffusion for target-aware molecule generation and affinity prediction
Guan, J., Qian, W. W., Peng, X., Su, Y., Peng, J., and Ma, J · 2023
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