Deep Confident Steps to New Pockets: Strategies for Docking
Generalization

Deep Confident Steps to New Pockets: Strategies for Docking Generalization

28 February 2024

Nicholas Polizzi

Regina Barzilay

Papers citing "Deep Confident Steps to New Pockets: Strategies for Docking Generalization"

15 / 15 papers shown

Title
PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking Yize Jiang Xinze Li Y. Zhang Jin Han Youjun Xu ... Yejin Choi Wu-Jun Li Tianfan Fu Fang Wu Junhong Liu 44 0 0 03 May 2025
EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions Ngoc-Quang Nguyen 35 0 0 07 Apr 2025
Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji Weinan E Linfeng Zhang Guolin Ke 48 0 0 20 Mar 2025
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation A. Singh Engin Tekin Maryam Nadeem Nancy A. ElNaker Mohammad Amaan Sayeed Natalia Vassilieva Boulbaba Ben Amor 53 1 0 20 Mar 2025
Fast and Accurate Blind Flexible Docking Zizhuo Zhang Lijun Wu Kaiyuan Gao Jiangchao Yao Tao Qin Bo Han 40 0 0 20 Feb 2025
Rao-Blackwell Gradient Estimators for Equivariant Denoising Diffusion Vinh Tong Trung-Dung Hoang Anji Liu Guy Van den Broeck Mathias Niepert DiffM 82 0 0 14 Feb 2025
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction Alex Morehead Jianlin Cheng OOD 117 2 0 14 Dec 2024
RapidDock: Unlocking Proteome-scale Molecular Docking Rafał Powalski Bazyli Klockiewicz Maciej Jaśkowski Bartosz Topolski Paweł Dąbrowski-Tumański Maciej Wiśniewski Łukasz Kuciński Piotr Miłoś Dariusz Plewczynski 29 0 0 16 Oct 2024
InstructBioMol: Advancing Biomolecule Understanding and Design Following Human Instructions Xiang Zhuang Keyan Ding Tianwen Lyu Yinuo Jiang Xiaotong Li ... Ming Qin Kehua Feng Jike Wang Qiang Zhang Huajun Chen 33 3 0 10 Oct 2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules Trevor Norton Debswapna Bhattacharya MedIm DiffM 50 2 0 31 May 2024
Deep Learning for Protein-Ligand Docking: Are We There Yet? Alex Morehead Nabin Giri Jian Liu Jianlin Cheng Jianlin Cheng OOD 40 4 0 23 May 2024
GeoDirDock: Guiding Docking Along Geodesic Paths Raúl Minán Javier Gallardo Álvaro Ciudad Alexis Molina DiffM 48 0 0 09 Apr 2024
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 38 1 0 20 Jun 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 142 412 0 04 Oct 2022
Riemannian Score-Based Generative Modelling Valentin De Bortoli Emile Mathieu M. Hutchinson James Thornton Yee Whye Teh Arnaud Doucet DiffM 222 165 0 06 Feb 2022