Protein sequence design with deep generative models

9 April 2021

Papers citing "Protein sequence design with deep generative models"

29 / 29 papers shown

Title
$α$ -TCVAE: On the relationship between Disentanglement and Diversity Cristian Meo Louis Mahon Anirudh Goyal Justin Dauwels DRL 61 8 0 01 Nov 2024
Conditional Enzyme Generation Using Protein Language Models with Adapters Jason Yang Aadyot Bhatnagar Jeffrey A. Ruffolo Ali Madani 26 4 0 04 Oct 2024
De novo antibody design with SE(3) diffusion Daniel Cutting Frédéric A. Dreyer David Errington Constantin Schneider Charlotte M. Deane DiffM 33 3 0 13 May 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 37 6 0 16 Feb 2024
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation Yongkang Wang Xuan Liu Feng Huang Zhankun Xiong Wen Zhang 52 14 0 25 Dec 2023
Best practices for machine learning in antibody discovery and development Leonard Wossnig Norbert Furtmann Andrew Buchanan Sandeep Kumar Victor Greiff 16 7 0 13 Dec 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 33 10 0 18 Oct 2023
De Novo Drug Design with Joint Transformers Adam Izdebski Ewelina Węglarz-Tomczak Ewa Szczurek Jakub M. Tomczak ViT 21 3 0 03 Oct 2023
Target-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning Haoxiang Luo Gang Sun 34 2 0 02 Aug 2023
Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement Zhangyang Gao Cheng Tan Stan Z. Li 23 15 0 20 May 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 18 31 0 06 May 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 33 0 0 05 Apr 2023
Diffusion map particle systems for generative modeling Fengyi Li Youssef Marzouk DiffM 13 4 0 01 Apr 2023
ProtFIM: Fill-in-Middle Protein Sequence Design via Protein Language Models Youhan Lee Hasun Yu 8 3 0 29 Mar 2023
Lightweight Contrastive Protein Structure-Sequence Transformation Jiangbin Zheng Ge Wang Yufei Huang Bozhen Hu Siyuan Li Cheng Tan Xinwen Fan Stan Z. Li 15 6 0 19 Mar 2023
A Text-guided Protein Design Framework Shengchao Liu Yanjing Li Zhuoxinran Li A. Gitter Yutao Zhu ... Arvind Ramanathan Chaowei Xiao Jian Tang Hongyu Guo Anima Anandkumar 67 61 0 09 Feb 2023
Feature Likelihood Divergence: Evaluating the Generalization of Generative Models Using Samples Marco Jiralerspong A. Bose I. Gemp Chongli Qin Yoram Bachrach Gauthier Gidel EGVM 29 5 0 09 Feb 2023
Target specific peptide design using latent space approximate trajectory collector Tong Lin Sijie Chen R. Basu D. Pei Xiaolin Cheng L. Kara 11 2 0 02 Feb 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 21 19 0 22 Jan 2023
Thompson Sampling with Diffusion Generative Prior Yu-Guan Hsieh S. Kasiviswanathan B. Kveton Patrick Blobaum DiffM 27 7 0 12 Jan 2023
Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC Patrick Emami Aidan Perreault Jeffrey N. Law David J. Biagioni Peter C. St. John 18 13 0 20 Dec 2022
PiFold: Toward effective and efficient protein inverse folding Zhangyang Gao Cheng Tan Pablo Chacón Stan Z. Li AI4CE 67 104 0 22 Sep 2022
Learning Hierarchical Protein Representations via Complete 3D Graph Networks Limei Wang Haoran Liu Yi Liu Jerry Kurtin Shuiwang Ji GNN 30 55 0 26 Jul 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modeling Jannis Born Matteo Manica 13 91 0 01 Feb 2022
Deep Generative Modeling for Protein Design Alexey Strokach Philip M. Kim AI4CE 179 90 0 31 Aug 2021
Deep Extrapolation for Attribute-Enhanced Generation Alvin Chan Ali Madani Ben Krause Nikhil Naik 19 24 0 07 Jul 2021
Adaptive machine learning for protein engineering B. Hie Kevin Kaichuang Yang 9 80 0 10 Jun 2021
Design by adaptive sampling David H. Brookes Jennifer Listgarten TPM 39 65 0 08 Oct 2018
Effective Approaches to Attention-based Neural Machine Translation Thang Luong Hieu H. Pham Christopher D. Manning 218 7,923 0 17 Aug 2015