ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design

no code implementations • 22 Oct 2024 • Keir Adams, Kento Abeywardane, Jenna Fromer, Connor W. Coley

Inspired by traditional ligand discovery, we compose 3D similarity scoring functions to assess ShEPhERD's ability to conditionally generate novel molecules with desired interaction profiles.

Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks

1 code implementation • 29 Sep 2023 • Yanqiao Zhu, Jeehyun Hwang, Keir Adams, Zhen Liu, Bozhao Nan, Brock Stenfors, Yuanqi Du, Jatin Chauhan, Olaf Wiest, Olexandr Isayev, Connor W. Coley, Yizhou Sun, Wei Wang

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design.

Drug Discovery Ensemble Learning +2

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

1 code implementation • 17 Jul 2023 • Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Haiyang Yu, Yuqing Xie, Xiang Fu, Alex Strasser, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik Bekkers, Michael Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess Smidt, Shuiwang Ji

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences.

Out-of-Distribution Generalization Transfer Learning +1

Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design

1 code implementation • 6 Oct 2022 • Keir Adams, Connor W. Coley

Shape-based virtual screening is widely employed in ligand-based drug design to search chemical libraries for molecules with similar 3D shapes yet novel 2D chemical structures compared to known ligands.

valid

Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations

1 code implementation • ICLR 2022 • Keir Adams, Lagnajit Pattanaik, Connor W. Coley

Molecular chirality, a form of stereochemistry most often describing relative spatial arrangements of bonded neighbors around tetrahedral carbon centers, influences the set of 3D conformers accessible to the molecule without changing its 2D graph connectivity.

Contrastive Learning Data Augmentation +3