Anna Vangone
Anna Vangone
Large Molecule Research - Roche
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Updates to the integrated protein–protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2
T Vreven, IH Moal, A Vangone, BG Pierce, PL Kastritis, M Torchala, ...
Journal of molecular biology 427 (19), 3031-3041, 2015
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
COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes
A Vangone, R Spinelli, V Scarano, L Cavallo, R Oliva
Bioinformatics 27 (20), 2915-2916, 2011
Contacts-based prediction of binding affinity in protein–protein complexes
A Vangone, AMJJ Bonvin
elife 4, e07454, 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
Survival kinase genes present prognostic significance in glioblastoma
RT Varghese, Y Liang, T Guan, CT Franck, DF Kelly, Z Sheng
Oncotarget 7 (15), 20140, 2016
Ranking multiple docking solutions based on the conservation of inter‐residue contacts
R Oliva, A Vangone, L Cavallo
Proteins: Structure, Function, and Bioinformatics 81 (9), 1571-1584, 2013
CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts
E Chermak, A Petta, L Serra, A Vangone, V Scarano, L Cavallo, R Oliva
Bioinformatics 31 (9), 1481-1483, 2015
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 (1), 175-185, 2018
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories
S Abdel-Azeim, E Chermak, A Vangone, R Oliva, L Cavallo
BMC bioinformatics 15 (S5), S1, 2014
CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions
A Vangone, R Oliva, L Cavallo
Bmc Bioinformatics 13 (S4), S19, 2012
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
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
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
Using a consensus approach based on the conservation of inter‐residue contacts to rank CAPRI models
A Vangone, L Cavallo, R Oliva
Proteins: Structure, Function, and Bioinformatics 81 (12), 2210-2220, 2013
Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes
C Geng, A Vangone, AMJJ Bonvin
Protein Engineering, Design and Selection 29 (8), 291-299, 2016
Structural basis for the recognition in an idiotype-anti-idiotype antibody complex related to celiac disease
A Vangone, S Abdel-Azeim, I Caputo, D Sblattero, R Di Niro, L Cavallo, ...
PLoS One 9 (7), e102839, 2014
PRODIGY: a contact-based predictor of binding affinity in protein-protein complexes
A Vangone, A Bonvin
Bio-protocol 7, e2124, 2017
A recurrent Gly43Asp substitution in coagulation Factor X rigidifies its catalytic pocket and impairs catalytic activity and intracellular trafficking
M Menegatti, A Vangone, R Palla, G Milano, L Cavallo, R Oliva, ...
Thrombosis Research 133 (3), 481-487, 2014
Fragment‐based modeling of membrane protein loops: Successes, failures, and prospects for the future
S Kelm, A Vangone, Y Choi, JP Ebejer, J Shi, CM Deane
Proteins: Structure, Function, and Bioinformatics 82 (2), 175-186, 2014
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