Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches. - 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 (Pacific Symposium on Biocomputing, 2008)

Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study. - Li C. Xue; Rafael A. Jordan; Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BCB, 2011)

Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results. - Li C. Xue; Rasna R. Walia; Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BCB, 2011)

HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods. - Li C. Xue; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2011)

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. - Li C. Xue; João P. G. L. M. Rodrigues; Panagiotis L. Kastritis; Alexandre M. J. J. Bonvin; Anna Vangone (Bioinform., 2016)

Template-based protein-protein docking exploiting pairwise interfacial residue restraints. - Li C. Xue; João P. G. L. M. Rodrigues; Drena Dobbs; Vasant G. Honavar; Alexandre M. J. J. Bonvin (Briefings Bioinform., 2017)

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. - 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; et al. (J. Comput. Aided Mol. Des., 2018)

Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. - Anna Vangone; Jörg Schaarschmidt; Panagiotis I. Koukos; Cunliang Geng; Nevia Citro; Mikael E. Trellet; Li C. Xue; Alexandre M. J. J. Bonvin (Bioinform., 2019)

Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. - Panagiotis I. Koukos; Li C. Xue; Alexandre M. J. J. Bonvin (J. Comput. Aided Mol. Des., 2019)

iScore: a novel graph kernel-based function for scoring protein-protein docking models. - Cunliang Geng; Yong Jung; Nicolas Renaud; Vasant G. Honavar; Alexandre M. J. J. Bonvin; Li C. Xue (Bioinform., 2020)

iScore: An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines. - Nicolas Renaud; Yong Jung; Vasant G. Honavar; Cunliang Geng; Alexandre M. J. J. Bonvin; Li C. Xue (SoftwareX, 2020)

DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces. - Manon Réau; Nicolas Renaud; Li C. Xue; Alexandre M. J. J. Bonvin (Bioinform., 2023)

GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations. - Daniel-T. Rademaker; Kevin J. van Geemen; Li C. Xue (Bioinform., 2023)

DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning. - 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 (J. Open Source Softw., 2024)