GraphGPSM: a global scoring model for protein structure using graph neural networks
G He, J Liu, D Liu, G Zhang - Briefings in bioinformatics, 2023 - academic.oup.com
The scoring models used for protein structure modeling and ranking are mainly divided into
unified field and protein-specific scoring functions. Although protein structure prediction has …
unified field and protein-specific scoring functions. Although protein structure prediction has …
iQDeep: an integrated web server for protein scoring using multiscale deep learning models
The remarkable recent advances in protein structure prediction have enabled computational
modeling of protein structures with considerably higher accuracy than ever before. While …
modeling of protein structures with considerably higher accuracy than ever before. While …
PersGNN: applying topological data analysis and geometric deep learning to structure-based protein function prediction
Understanding protein structure-function relationships is a key challenge in computational
biology, with applications across the biotechnology and pharmaceutical industries. While it …
biology, with applications across the biotechnology and pharmaceutical industries. While it …
3D-equivariant graph neural networks for protein model quality assessment
Motivation Quality assessment (QA) of predicted protein tertiary structure models plays an
important role in ranking and using them. With the recent development of deep learning end …
important role in ranking and using them. With the recent development of deep learning end …
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15
J Liu, D Liu, G He, G Zhang - Proteins: Structure, Function, and …, 2023 - Wiley Online Library
This article reports and analyzes the results of protein complex model accuracy estimation
by our methods (DeepUMQA3 and GraphGPSM) in the 15th Critical Assessment of …
by our methods (DeepUMQA3 and GraphGPSM) in the 15th Critical Assessment of …
Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information
P Jiao, B Wang, X Wang, B Liu, Y Wang, J Li - Bioinformatics, 2023 - academic.oup.com
Motivation In recent years, there has been a breakthrough in protein structure prediction,
and the AlphaFold2 model of the DeepMind team has improved the accuracy of protein …
and the AlphaFold2 model of the DeepMind team has improved the accuracy of protein …
Predicting residue‐specific qualities of individual protein models using residual neural networks and graph neural networks
The estimation of protein model accuracy (EMA) or model quality assessment (QA) is
important for protein structure prediction. An accurate EMA algorithm can guide the …
important for protein structure prediction. An accurate EMA algorithm can guide the …
[HTML][HTML] EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks
Reliable and accurate methods of estimating the accuracy of predicted protein models are
vital to understanding their respective utility. Discerning how the quaternary structure …
vital to understanding their respective utility. Discerning how the quaternary structure …
ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm
J Shao, B Liu - Briefings in Bioinformatics, 2021 - academic.oup.com
As one of the most important tasks in protein structure prediction, protein fold recognition has
attracted more and more attention. In this regard, some computational predictors have been …
attracted more and more attention. In this regard, some computational predictors have been …
A global machine learning based scoring function for protein structure prediction
E Faraggi, A Kloczkowski - Biophysical Journal, 2014 - cell.com
656a Wednesday, February 19, 2014 previous problems associated with knowledge-based
potentials. These features were obtained for a large set of native and decoy structures and a …
potentials. These features were obtained for a large set of native and decoy structures and a …