Li C. Xue

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 10

Top Topics

Grand Challenge

Protein Structure

Top Venues

J. Comput. Aided Mol. Des.

Briefings Bioinform.

Publications

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) (2024)
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)
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)
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 (2020)
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) (2020)
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) (2019)
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) (2019)
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) (2018)
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) (2017)
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) (2016)
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)
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)
Li C. Xue, Drena Dobbs, Vasant G. Honavar
HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods. BMC Bioinform. 12 (2011)
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)