Articles with public access mandates - Li C XueLearn more
Available somewhere: 23
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: US National Institutes of Health
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: US National Science Foundation, US National Institutes of Health …
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
Mandates: US National Science Foundation, US National Institutes of Health, Canadian …
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: US National Institutes of Health
HomPPI: a class of sequence homology based protein-protein interface prediction methods
LC Xue, D Dobbs, V Honavar
BMC bioinformatics 12, 1-24, 2011
Mandates: US National Institutes of Health
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces
M Réau, N Renaud, LC Xue, AMJJ Bonvin
Bioinformatics 39 (1), btac759, 2023
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: US National Science Foundation, US National Institutes of Health …
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: Netherlands Organisation for Scientific Research, European Commission
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
Mandates: US National Institutes of Health
Template-based protein–protein docking exploiting pairwise interfacial residue restraints
LC Xue, JP Rodrigues, D Dobbs, V Honavar, AMJJ Bonvin
Briefings in bioinformatics 18 (3), 458-466, 2017
Mandates: US National Institutes of Health, Netherlands Organisation for Scientific …
An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45
PI Koukos, J Roel‐Touris, F Ambrosetti, C Geng, J Schaarschmidt, ...
Proteins: Structure, Function, and Bioinformatics 88 (8), 1029-1036, 2020
Mandates: Netherlands Organisation for Scientific Research, Fundação para a Ciência e …
Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study
LC Xue, RA Jordan, Y El-Manzalawy, D Dobbs, V Honavar
Proceedings of the 2nd ACM conference on bioinformatics, computational …, 2011
Mandates: US National Institutes of Health
The solution structure of the kallikrein-related peptidases inhibitor SPINK6
S Jung, J Fischer, B Spudy, T Kerkow, FD Sönnichsen, L Xue, ...
Biochemical and biophysical research communications 471 (1), 103-108, 2016
Mandates: Austrian Science Fund, German Research Foundation, Netherlands Organisation …
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