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Joana Pereira
Joana Pereira
Other namesJoana Soares Pereira, Joana Maria Soares Pereira
Postdoctoral researcher, Biozentrum, University of Basel
Verified email at unibas.ch
Title
Cited by
Cited by
Year
Comparative genomics reveals insights into avian genome evolution and adaptation
G Zhang, C Li, Q Li, B Li, DM Larkin, C Lee, JF Storz, A Antunes, ...
Science 346 (6215), 1311-1320, 2014
10242014
High‐accuracy protein structure prediction in CASP14
J Pereira, AJ Simpkin, MD Hartmann, DJ Rigden, RM Keegan, AN Lupas
Proteins: Structure, Function, and Bioinformatics 89 (12), 1687-1699, 2021
2392021
The CCP4 suite: integrative software for macromolecular crystallography
J Agirre, M Atanasova, H Bagdonas, CB Ballard, A Baslé, ...
Acta Crystallographica Section D: Structural Biology 79 (6), 449-461, 2023
1152023
The breakthrough in protein structure prediction
AN Lupas, J Pereira, V Alva, F Merino, M Coles, MD Hartmann
Biochemical journal 478 (10), 1885-1890, 2021
462021
Assessing the utility of CASP14 models for molecular replacement
C Millán, RM Keegan, J Pereira, MD Sammito, AJ Simpkin, AJ McCoy, ...
Proteins: Structure, Function, and Bioinformatics 89 (12), 1752-1769, 2021
422021
Evolutionary genomics and adaptive evolution of the hedgehog gene family (shh, ihh and dhh) in vertebrates
J Pereira, WE Johnson, SJ O’Brien, ED Jarvis, G Zhang, MTP Gilbert, ...
PLoS ONE 9 (12), 1-35, 2014
402014
Sequence assignment for low-resolution modelling of protein crystal structures
G Chojnowski, J Pereira, VS Lamzin
Acta Crystallographica Section D: Structural Biology 75 (8), 753-763, 2019
302019
Uncovering new families and folds in the natural protein universe
J Durairaj, AM Waterhouse, T Mets, T Brodiazhenko, M Abdullah, ...
Nature 622 (7983), 646-653, 2023
28*2023
The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution
G Chojnowski, K Choudhury, P Heuser, E Sobolev, J Pereira, ...
Acta Crystallographica Section D: Structural Biology 76 (3), 248-260, 2020
212020
The origin of mitochondria-specific outer membrane β-barrels from an ancestral bacterial fragment
J Pereira, AN Lupas
Genome biology and evolution 10 (10), 2759-2765, 2018
172018
A distance geometry-based description and validation of protein main-chain conformation
J Pereira, VS Lamzin
IUCRj 4 (5), 2017
172017
Estimation of the protein-ligand interaction energy for model building and validation
DA Beshnova, J Pereira, VS Lamzin
Acta Crystallographica Section D 73, 195-202, 2017
132017
The Ancestral KH Peptide at the Root of a Domain Family With Three Different Folds
J Pereira, AN Lupas
Bioinformatics, 2018
122018
How do I get the most out of my protein sequence using bioinformatics tools?
J Pereira, V Alva
Acta Crystallographica Section D: Structural Biology 77 (9), 1116-1126, 2021
102021
Gram-negative outer-membrane proteins with multiple β-barrel domains
R Solan, J Pereira, AN Lupas, R Kolodny, N Ben-Tal
Proceedings of the National Academy of Sciences 118 (31), e2104059118, 2021
102021
GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts
J Pereira
Journal of Molecular Biology 433 (11), 166943, 2021
52021
Building atomic models into electron microscopy maps with ARP/wARP version 8.0
G Chojnowski, P Heuser, J Pereira, V Lamzin
Acta Crystallographica Section A: Foundations and Advances 74, e151-e151, 2018
52018
The VCBS superfamily forms a third supercluster of β-propellers that includes tachylectin and integrins
J Pereira, AN Lupas
Bioinformatics 36 (24), 5618-5622, 2020
42020
Interactomes in the era of deep learning
J Pereira, T Schwede
Science 374 (6573), 1319-1320, 2021
32021
New β-propellers are continuously amplified from single blades in all major lineages of the β-propeller superfamily
J Pereira, AN Lupas
Frontiers in Molecular Biosciences 9, 895496, 2022
12022
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Articles 1–20