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2020 – today
- 2024
[j11]Giulia Crocioni
, Dani L. Bodor, Coos Baakman, Farzaneh M. Parizi, Daniel-T. Rademaker, Gayatri Ramakrishnan, Sven van der Burg, Dario F. Marzella, João M. C. Teixeira, Li C. Xue:
DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning. J. Open Source Softw. 9(96): 5983 (2024)- 2023
- [j10]Manon Réau, Nicolas Renaud, Li C. Xue, Alexandre M. J. J. Bonvin:
DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces. Bioinform. 39(1) (2023) - [j9]Daniel-T. Rademaker, Kevin J. van Geemen, Li C. Xue:
GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations. Bioinform. 39(8) (2023) - 2020
- [j8]Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant G. Honavar, Alexandre M. J. J. Bonvin, Li C. Xue:
iScore: a novel graph kernel-based function for scoring protein-protein docking models. Bioinform. 36(1): 112-121 (2020) - [j7]Nicolas Renaud, Yong Jung, Vasant G. Honavar, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue:
iScore: An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines. SoftwareX 11: 100462 (2020)
2010 – 2019
- 2019
- [j6]Anna Vangone, Jörg Schaarschmidt, Panagiotis I. Koukos, Cunliang Geng, Nevia Citro, Mikael E. Trellet, Li C. Xue, Alexandre M. J. J. Bonvin:
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinform. 35(9): 1585-1587 (2019) - [j5]Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin:
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. J. Comput. Aided Mol. Des. 33(1): 83-91 (2019) - 2018
- [j4]Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, Alexandre M. J. J. Bonvin:
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J. Comput. Aided Mol. Des. 32(1): 175-185 (2018) - 2017
- [j3]Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs, Vasant G. Honavar, Alexandre M. J. J. Bonvin:
Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings Bioinform. 18(3): 458-466 (2017) - 2016
- [j2]Li C. Xue, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Anna Vangone:
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinform. 32(23): 3676-3678 (2016) - 2011
- [j1]Li C. Xue, Drena Dobbs, Vasant G. Honavar:
HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods. BMC Bioinform. 12: 244 (2011) - [c3]Li C. Xue, Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar:
Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study. BCB 2011: 441-445 - [c2]Li C. Xue, Rasna R. Walia, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar:
Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results. BCB 2011: 556-558
2000 – 2009
- 2008
- [c1]Jae-Hyung Lee, Michael Hamilton, Colin Gleeson, Cornelia Caragea, Peter Zaback, Jeffry D. Sander, Li C. Xue, Feihong Wu, Michael Terribilini, Vasant G. Honavar, Drena Dobbs:
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches. Pacific Symposium on Biocomputing 2008: 501-512
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