HomPPI: a class of sequence homology based protein-protein interface prediction methods

por Xue, Li C, Dobbs, Drena, Honavar, Vasant
Publicado 2011

GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations

por Rademaker, Daniel T, van Geemen, Kevin J, Xue, Li C
Publicado 2023

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3

por Koukos, Panagiotis I., Xue, Li C., Bonvin, Alexandre M. J. J.
Publicado 2018

Entropy and Variability: A Second Opinion by Deep Learning

por Rademaker, Daniel T., Xue, Li C., ‘t Hoen, Peter A. C., Vriend, Gert
Publicado 2022

DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces

por Réau, Manon, Renaud, Nicolas, Xue, Li C, Bonvin, Alexandre M J J
Publicado 2022

RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins

por Walia, Rasna R., Xue, Li C., Wilkins, Katherine, El-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant
Publicado 2014

iSEE: Interface structure, evolution, and energy‐based machine learning predictor of binding affinity changes upon mutations

por Geng, Cunliang, Vangone, Anna, Folkers, Gert E., Xue, Li C., Bonvin, Alexandre M. J. J.
Publicado 2018

MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein–Protein Docking Conformations

por Jung, Yong, Geng, Cunliang, Bonvin, Alexandre M. J. J., Xue, Li C., Honavar, Vasant G.
Publicado 2023

iScore: a novel graph kernel-based function for scoring protein–protein docking models

por Geng, Cunliang, Jung, Yong, Renaud, Nicolas, Honavar, Vasant, Bonvin, Alexandre M J J, Xue, Li C
Publicado 2020

iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

por Renaud, Nicolas, Jung, Yong, Honavar, Vasant, Geng, Cunliang, Bonvin, Alexandre M.J.J., Xue, Li C.
Publicado 2020

Template-based protein–protein docking exploiting pairwise interfacial residue restraints

por Xue, Li C, Rodrigues, João P G L M, Dobbs, Drena, Honavar, Vasant, Bonvin, Alexandre M J J
Publicado 2017

Understanding structure-guided variant effect predictions using 3D convolutional neural networks

por Ramakrishnan, Gayatri, Baakman, Coos, Heijl, Stephan, Vroling, Bas, van Horck, Ragna, Hiraki, Jeffrey, Xue, Li C., Huynen, Martijn A.
Publicado 2023

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

por Renaud, Nicolas, Geng, Cunliang, Georgievska, Sonja, Ambrosetti, Francesco, Ridder, Lars, Marzella, Dario F., Réau, Manon F., Bonvin, Alexandre M. J. J., Xue, Li C.
Publicado 2021

PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes

por Marzella, Dario F., Parizi, Farzaneh M., van Tilborg, Derek, Renaud, Nicolas, Sybrandi, Daan, Buzatu, Rafaella, Rademaker, Daniel T., ‘t Hoen, Peter A. C., Xue, Li C.
Publicado 2022

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

por Kurkcuoglu, Zeynep, Koukos, Panagiotis I., Citro, Nevia, Trellet, Mikael E., Rodrigues, J. P. G. L. M., Moreira, Irina S., Roel-Touris, Jorge, Melquiond, Adrien S. J., Geng, Cunliang, Schaarschmidt, Jörg, Xue, Li C., Vangone, Anna, Bonvin, A. M. J. J.
Publicado 2017