Diffusion models: A comprehensive survey of methods and applications

L Yang, Z Zhang, Y Song, S Hong, R Xu, Y Zhao… - ACM Computing …, 2023 - dl.acm.org
Diffusion models have emerged as a powerful new family of deep generative models with
record-breaking performance in many applications, including image synthesis, video …

Scientific large language models: A survey on biological & chemical domains

Q Zhang, K Ding, T Lv, X Wang, Q Yin, Y Zhang… - ACM Computing …, 2024 - dl.acm.org
Large Language Models (LLMs) have emerged as a transformative power in enhancing
natural language comprehension, representing a significant stride toward artificial general …

Accurate structure prediction of biomolecular interactions with AlphaFold 3

J Abramson, J Adler, J Dunger, R Evans, T Green… - Nature, 2024 - nature.com
The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of
proteins and their interactions, enabling a huge range of applications in protein modelling …

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh… - Science, 2024 - science.org
Deep-learning methods have revolutionized protein structure prediction and design but are
presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which …

An artificial intelligence accelerated virtual screening platform for drug discovery

G Zhou, DV Rusnac, H Park, D Canzani… - Nature …, 2024 - nature.com
Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing
interest in the screening of multi-billion chemical compound libraries. However, the success …

Enhancing activity prediction models in drug discovery with the ability to understand human language

P Seidl, A Vall, S Hochreiter… - … on Machine Learning, 2023 - proceedings.mlr.press
Activity and property prediction models are the central workhorses in drug discovery and
materials sciences, but currently, they have to be trained or fine-tuned for new tasks. Without …

Application of computational biology and artificial intelligence in drug design

Y Zhang, M Luo, P Wu, S Wu, TY Lee, C Bai - International journal of …, 2022 - mdpi.com
Traditional drug design requires a great amount of research time and developmental
expense. Booming computational approaches, including computational biology, computer …

A review of large language models and autonomous agents in chemistry

MC Ramos, CJ Collison, AD White - Chemical Science, 2025 - pubs.rsc.org
Large language models (LLMs) have emerged as powerful tools in chemistry, significantly
impacting molecule design, property prediction, and synthesis optimization. This review …

Git-mol: A multi-modal large language model for molecular science with graph, image, and text

P Liu, Y Ren, J Tao, Z Ren - Computers in biology and medicine, 2024 - Elsevier
Large language models have made significant strides in natural language processing,
enabling innovative applications in molecular science by processing textual representations …

Drugclip: Contrasive protein-molecule representation learning for virtual screening

B Gao, B Qiang, H Tan, Y Jia, M Ren… - Advances in …, 2024 - proceedings.neurips.cc
Virtual screening, which identifies potential drugs from vast compound databases to bind
with a particular protein pocket, is a critical step in AI-assisted drug discovery. Traditional …