| 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 | 1164 | 2014 |
| The CCP4 suite: integrative software for macromolecular crystallography J Agirre, M Atanasova, H Bagdonas, CB Ballard, A Baslé, ... Biological Crystallography 79 (6), 449-461, 2023 | 774 | 2023 |
| 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 | 380 | 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 | 161 | 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 | 74 | 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 | 62 | 2021 |
| 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 | 48 | 2014 |
| 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 | 46* | 2022 |
| Sequence assignment for low-resolution modelling of protein crystal structures G Chojnowski, J Pereira, VS Lamzin Biological Crystallography 75 (8), 753-763, 2019 | 33 | 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, ... Biological Crystallography 76 (3), 248-260, 2020 | 27 | 2020 |
| GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts J Pereira Journal of Molecular Biology 433 (11), 166943, 2021 | 20 | 2021 |
| 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 | 19 | 2018 |
| A distance geometry-based description and validation of protein main-chain conformation J Pereira, VS Lamzin IUCRj 4 (5), 2017 | 19 | 2017 |
| The SWISS‐model repository of 3D protein structures and models X Robin, AM Waterhouse, S Bienert, G Studer, LT Alexander, G Tauriello, ... Open Access Databases and Datasets for Drug Discovery, 175-199, 2024 | 17 | 2024 |
| 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 | 16 | 2021 |
| 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 | 16 | 2021 |
| The Ancestral KH Peptide at the Root of a Domain Family With Three Different Folds J Pereira, AN Lupas Bioinformatics, 2018 | 14 | 2018 |
| 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 | 14 | 2017 |
| Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study J Durairaj, OM Follonier, K Leuzinger, LT Alexander, M Wilhelm, J Pereira, ... Msphere 9 (4), e00799-23, 2024 | 13 | 2024 |
| The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes R Odai, M Leemann, T Al-Murad, M Abdullah, L Shyrokova, T Tenson, ... Science Advances 11 (40), eadz8560, 2025 | 10 | 2025 |
Andrei LupasDirector of the Department of Protein Evolution, Max-Planck-Institute for BiologyVerified email at tuebingen.mpg.de
