Knowledge-Design: Pushing the Limit of Protein Design via Knowledge
Refinement

Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement

20 May 2023

Cheng Tan

Stan Z. Li

Papers citing "Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement"

15 / 15 papers shown

Title
Improving Inverse Folding for Peptide Design with Diversity-regularized Direct Preference Optimization Ryan Park Darren J. Hsu C. Brian Roland Maria Korshunova Chen Tessler Shie Mannor Olivia Viessmann Bruno Trentini 19 1 0 25 Oct 2024
DPLM-2: A Multimodal Diffusion Protein Language Model X. Wang Zaixiang Zheng Fei Ye Dongyu Xue Shujian Huang Quanquan Gu 15 13 0 17 Oct 2024
Generative AI for Controllable Protein Sequence Design: A Survey Yiheng Zhu Zitai Kong Jialun Wu Weize Liu Yuqiang Han Mingze Yin Hongxia Xu Chang-Yu Hsieh Tingjun Hou AI4CE 33 6 0 16 Feb 2024
FoldToken: Learning Protein Language via Vector Quantization and Beyond Zhangyang Gao Cheng Tan Jue Wang Yufei Huang Lirong Wu Stan Z. Li 15 9 0 04 Feb 2024
Efficiently Predicting Protein Stability Changes Upon Single-point Mutation with Large Language Models Yijie Zhang Zhangyang Gao Cheng Tan Stan Z.Li 17 2 0 07 Dec 2023
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design Chuanrui Wang Bozitao Zhong Zuobai Zhang Narendra Chaudhary Sanchit Misra Jian Tang 12 5 0 30 Nov 2023
De novo protein design using geometric vector field networks Weian Mao Muzhi Zhu Zheng Sun Shuaike Shen Lin Yuanbo Wu Hao Chen Chunhua Shen DiffM 17 10 0 18 Oct 2023
Generative artificial intelligence for de novo protein design Adam Winnifrith C. Outeiral Brian L. Hie AI4CE 19 13 0 15 Oct 2023
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola 18 24 0 09 Oct 2023
RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design Cheng Tan Yijie Zhang Zhangyang Gao Bozhen Hu Siyuan Li Zicheng Liu Stan Z. Li 17 5 0 25 Jan 2023
PiFold: Toward effective and efficient protein inverse folding Zhangyang Gao Cheng Tan Pablo Chacón Stan Z. Li AI4CE 59 104 0 22 Sep 2022
AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB Zhangyang Gao Cheng Tan Stan Z. Li 129 52 0 01 Feb 2022
OntoProtein: Protein Pretraining With Gene Ontology Embedding Ningyu Zhang Zhen Bi Xiaozhuan Liang Shuyang Cheng Haosen Hong Shumin Deng J. Lian Qiang Zhang Huajun Chen 85 86 0 23 Jan 2022
Deep Generative Modeling for Protein Design Alexey Strokach Philip M. Kim AI4CE 160 90 0 31 Aug 2021
Densely Connected Convolutional Networks Gao Huang Zhuang Liu L. V. D. van der Maaten Kilian Q. Weinberger PINN 3DV 236 35,884 0 25 Aug 2016