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 | 1057 | 2014 |
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 | 273 | 2021 |
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 | 189 | 2023 |
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 | 49 | 2021 |
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 | 46 | 2021 |
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 | 40* | 2023 |
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 | 40 | 2014 |
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 | 31 | 2019 |
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 | 24 | 2020 |
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 | 17 | 2018 |
A distance geometry-based description and validation of protein main-chain conformation J Pereira, VS Lamzin IUCRj 4 (5), 2017 | 17 | 2017 |
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 | 13 | 2017 |
The Ancestral KH Peptide at the Root of a Domain Family With Three Different Folds J Pereira, AN Lupas Bioinformatics, 2018 | 12 | 2018 |
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 | 11 | 2021 |
How do I get the most out of my protein sequence using bioinformatics tools? J Pereira, V Alva Biological Crystallography 77 (9), 1116-1126, 2021 | 10 | 2021 |
Embedding-based alignment: combining protein language models and alignment approaches to detect structural similarities in the twilight-zone L Pantolini, G Studer, J Pereira, J Durairaj, T Schwede bioRxiv, 2022.12. 13.520313, 2022 | 6* | 2022 |
GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts J Pereira Journal of Molecular Biology 433 (11), 166943, 2021 | 6 | 2021 |
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 | 5 | 2018 |
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 | 4 | 2020 |
Interactomes in the era of deep learning J Pereira, T Schwede Science 374 (6573), 1319-1320, 2021 | 3 | 2021 |