Accelerating the integration of ChatGPT and other large‐scale AI models into biomedical research and healthcare

DQ Wang, LY Feng, JG Ye, JG Zou… - MedComm–Future …, 2023 - Wiley Online Library
Large‐scale artificial intelligence (AI) models such as ChatGPT have the potential to
improve performance on many benchmarks and real‐world tasks. However, it is difficult to …

Growing ecosystem of deep learning methods for modeling protein–protein interactions

JR Rogers, G Nikolényi… - … Engineering, Design and …, 2023 - academic.oup.com
Numerous cellular functions rely on protein–protein interactions. Efforts to comprehensively
characterize them remain challenged however by the diversity of molecular recognition …

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15

RS Roy, J Liu, N Giri, Z Guo… - … : Structure, Function, and …, 2023 - Wiley Online Library
Estimating the accuracy of quaternary structural models of protein complexes and
assemblies (EMA) is important for predicting quaternary structures and applying them to …

ComplexQA: A deep graph learning approach for protein complex structure assessment

L Zhang, S Wang, J Hou, D Si, J Zhu… - Briefings in …, 2023 - academic.oup.com
Motivation In recent years, the end-to-end deep learning method for single-chain protein
structure prediction has achieved high accuracy. For example, the state-of-the-art method …

Protein structure accuracy estimation using geometry‐complete perceptron networks

A Morehead, J Liu, J Cheng - Protein Science, 2024 - Wiley Online Library
Estimating the accuracy of protein structural models is a critical task in protein bioinformatics.
The need for robust methods in the estimation of protein model accuracy (EMA) is prevalent …

Chemical cross-linking and mass spectrometry enabled systems-level structural biology

L Botticelli, AA Bakhtina, NK Kaiser, A Keller… - Current Opinion in …, 2024 - Elsevier
Structural information on protein–protein interactions (PPIs) is essential for improved
understanding of regulatory interactome networks that confer various physiological and …

[HTML][HTML] AlphaFold Accurately Predicts the Structure of Ribosomally Synthesized and Post-Translationally Modified Peptide Biosynthetic Enzymes

CH Gordon, E Hendrix, Y He, MC Walker - Biomolecules, 2023 - mdpi.com
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing
class of natural products biosynthesized from a genetically encoded precursor peptide. The …

[HTML][HTML] EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks

AJ Siciliano, C Zhao, T Liu, Z Wang - International Journal of Molecular …, 2024 - mdpi.com
Reliable and accurate methods of estimating the accuracy of predicted protein models are
vital to understanding their respective utility. Discerning how the quaternary structure …

[HTML][HTML] A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models

X Chen, J Liu, N Park, J Cheng - Biomolecules, 2024 - mdpi.com
The quality prediction of quaternary structure models of a protein complex, in the absence of
its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for …

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15.

J Cheng, RS Roy, J Liu, N Giri, Z Guo - Biorxiv: the Preprint Server …, 2023 - europepmc.org
Estimating the accuracy of quaternary structural models of protein complexes and
assemblies (EMA) is important for predicting quaternary structures and applying them to …