Li C Xue
Li C Xue
Radboud University Medical Center
Verified email at - Homepage
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PRODIGY: a web server for predicting the binding affinity of protein–protein complexes
LC Xue, JP Rodrigues, PL Kastritis, AM Bonvin, A Vangone
Bioinformatics 32 (23), 3676-3678, 2016
Computational prediction of protein interfaces: A review of data driven methods
LC Xue, D Dobbs, AMJJ Bonvin, V Honavar
FEBS letters 589 (23), 3516-3526, 2015
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment
MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ...
Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016
HomPPI: a class of sequence homology based protein-protein interface prediction methods
LC Xue, D Dobbs, V Honavar
BMC bioinformatics 12 (1), 1-24, 2011
Large-scale prediction of binding affinity in protein–small ligand complexes: The PRODIGY-LIG web server
A Vangone, J Schaarschmidt, P Koukos, C Geng, N Citro, ME Trellet, ...
Bioinformatics 35 (9), 1585-1587, 2019
RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins
RR Walia, LC Xue, K Wilkins, Y El-Manzalawy, D Dobbs, V Honavar
PloS one 9 (5), e97725, 2014
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
Z Kurkcuoglu, PI Koukos, N Citro, ME Trellet, J Rodrigues, IS Moreira, ...
Journal of computer-aided molecular design 32, 175-185, 2018
The simultaneous effect of polymer chemistry and device geometry on the in vitro activation of murine dendritic cells
LK Petersen, L Xue, MJ Wannemuehler, K Rajan, B Narasimhan
Biomaterials 30 (28), 5131-5142, 2009
Using Fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types
H Liu, J Yang, M Wang, L Xue, KC Chou
The Protein Journal 24, 385-389, 2005
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment
MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, ...
Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
C Geng, LC Xue, J Roel‐Touris, AMJJ Bonvin
Wiley Interdisciplinary Reviews: Computational Molecular Science 9 (5), e1410, 2019
Machine learning competition in immunology-prediction of HLA class I molecules
GL Zhang, HR Ansari, P Bradley, GC Cawley, T Hertz, X Hu, N Jojic, ...
J. Immunol. Methods 374 (1-2), 1-4, 2011
Feature selection for multi-class problems using support vector machines
GZ Li, J Yang, GP Liu, L Xue
PRICAI 2004: Trends in Artificial Intelligence: 8th Pacific Rim …, 2004
iSEE: Interface structure, evolution, and energy‐based machine learning predictor of binding affinity changes upon mutations
C Geng, A Vangone, GE Folkers, LC Xue, AMJJ Bonvin
Proteins: Structure, Function, and Bioinformatics 87 (2), 110-119, 2019
iScore: a novel graph kernel-based function for scoring protein–protein docking models
C Geng, Y Jung, N Renaud, V Honavar, AMJJ Bonvin, LC Xue
Bioinformatics 36 (1), 112-121, 2020
Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1
A Vangone, J Rodrigues, LC Xue, GCP van Zundert, C Geng, ...
Proteins: Structure, Function, and Bioinformatics 85 (3), 417-423, 2017
DockRank: Ranking docked conformations using partner‐specific sequence homology‐based protein interface prediction
LC Xue, RA Jordan, ELM Yasser, D Dobbs, V Honavar
Proteins: Structure, Function, and Bioinformatics 82 (2), 250-267, 2014
Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
PI Koukos, LC Xue, AMJJ Bonvin
Journal of computer-aided molecular design 33, 83-91, 2019
DeepRank: a deep learning framework for data mining 3D protein-protein interfaces
N Renaud, C Geng, S Georgievska, F Ambrosetti, L Ridder, DF Marzella, ...
Nature communications 12 (1), 7068, 2021
Identifying factors controlling protein release from combinatorial biomaterial libraries via hybrid data mining methods
X Li, L Petersen, S Broderick, B Narasimhan, K Rajan
ACS combinatorial science 13 (1), 50-58, 2011
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