Amelie Stein
3did: a catalog of domain-based interactions of known three-dimensional structure
R Mosca, A Ceol, A Stein, R Olivella, P Aloy
Nucleic acids research 42 (D1), D374-D379, 2014
3did: interacting protein domains of known three-dimensional structure
A Stein, RB Russell, P Aloy
Nucleic acids research 33 (suppl_1), D413-D417, 2005
Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta
MJ O’Meara, A Leaver-Fay, MD Tyka, A Stein, K Houlihan, F DiMaio, ...
Journal of chemical theory and computation 11 (2), 609-622, 2015
Improvements to robotics-inspired conformational sampling in rosetta
A Stein, T Kortemme
PloS one 8 (5), e63090, 2013
3did: identification and classification of domain-based interactions of known three-dimensional structure
A Stein, A Ceol, P Aloy
Nucleic acids research 39 (suppl_1), D718-D723, 2010
Contextual specificity in peptide-mediated protein interactions
A Stein, P Aloy
PloS one 3 (7), e2524, 2008
Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence
DR Littler, M Alvarez-Fernandez, A Stein, RG Hibbert, T Heidebrecht, ...
Nucleic acids research 38 (13), 4527-4538, 2010
Dynamic interactions of proteins in complex networks: a more structured view
A Stein, RA Pache, P Bernadó, M Pons, P Aloy
The FEBS journal 276 (19), 5390-5405, 2009
Three-dimensional modeling of protein interactions and complexes is going ‘omics
A Stein, R Mosca, P Aloy
Current opinion in structural biology 21 (2), 200-208, 2011
3did Update: domain–domain and peptide-mediated interactions of known 3D structure
A Stein, A Panjkovich, P Aloy
Nucleic acids research 37 (suppl_1), D300-D304, 2009
Biophysical and mechanistic models for disease-causing protein variants
A Stein, DM Fowler, R Hartmann-Petersen, K Lindorff-Larsen
Trends in biochemical sciences 44 (7), 575-588, 2019
Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair
GT Kapp, S Liu, A Stein, DT Wong, A Reményi, BJ Yeh, JS Fraser, ...
Proceedings of the National Academy of Sciences 109 (14), 5277-5282, 2012
Uncovering new substrates for Aurora A kinase
T Sardon, RA Pache, A Stein, H Molina, I Vernos, P Aloy
EMBO reports 11 (12), 977-984, 2010
Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations
SV Nielsen, A Stein, AB Dinitzen, E Papaleo, MH Tatham, EG Poulsen, ...
PLoS Genetics 13 (4), e1006739, 2017
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures
A Stein, P Aloy
PLoS computational biology 6 (5), e1000789, 2010
A structural biology community assessment of AlphaFold 2 applications
M Akdel, DEV Pires, EP Pardo, J Jänes, AO Zalevsky, B Mészáros, ...
BioRxiv, 2021
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks
A Stein, M Rueda, A Panjkovich, M Orozco, P Aloy
Structure 19 (6), 881-889, 2011
Approved drug mimics of short peptide ligands from protein interaction motifs
L Parthasarathi, F Casey, A Stein, P Aloy, DC Shields
Journal of chemical information and modeling 48 (10), 1943-1948, 2008
Toward mechanistic models for genotype–phenotype correlations in phenylketonuria using protein stability calculations
R Scheller, A Stein, SV Nielsen, FI Marin, AM Gerdes, M Di Marco, ...
Human mutation 40 (4), 444-457, 2019
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