Publications of J Pereira

Pereira, J.; Lupas, A.: New β-Propellers Are Continuously Amplified From Single Blades in all Major Lineages of the β-Propeller Superfamily. Frontiers in Molecular Biosciences 9, 895496 (2022)

Pereira, J.; Alva, V.: How do I get the most out of my protein sequence using bioinformatics tools? Acta Crystallographica Section D: Structural Biology 77 (9), pp. 1116 - 1126 (2021)

Solan, R.; Pereira, J.; Lupas, A.; Kolodny, R.; Ben-Tal, N.: Gram-negative outer-membrane proteins with multiple β-barrel domains. Proceedings of the National Academy of Sciences of the United States of America 118 (31), e2104059118 (2021)

Lupas, A.; Pereira, J.; Alva, V.; Merino, F.; Coles, M.; Hartmann, M.: The breakthrough in protein structure prediction. Biochemical Journal 478 (10), pp. 1885 - 1890 (2021)

Pereira, J.: GCsnap: Interactive Snapshots for the Comparison of Protein-Coding Genomic Contexts. Journal of Molecular Biology 433 (11), 166943 (2021)

Pereira, J.; Lupas, A.: The VCBS superfamily forms a third supercluster of β-propellers that includes tachylectin and integrins. Bioinformatics 36 (24), pp. 5618 - 5622 (2021)

Pereira, J.; Lupas, A.: The ancestral KH peptide at the root of a domain family with three different folds. Bioinformatics 34 (23), pp. 3961 - 3965 (2018)

Pereira, J.; Lupas, A.: The Origin of Mitochondria-Specific Outer Membrane beta-Barrels from an Ancestral Bacterial Fragment. Genome Biology and Evolution 10 (10), pp. 2759 - 2765 (2018)

Pereira, J.; Lupas, A.: The Origin of Mitochondria-Specific Outer Membrane β-Barrels from an Ancestral Bacterial Fragment. Genome Biology and Evolution 10 (10), pp. 2759 - 2765 (2018)

Millán, C.; Keegan, R.; Pereira, J.; Sammito, M.; Simpkin, A.; McCoy, A.; Lupas, A.; Hartmann, M.; Rigden, D.; Read, R.: Assessing the utility of CASP14 models for molecular replacement. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), 2020-05 - 2020-09. Proteins: Structure, Function, and Bioinformatics 89 (12), pp. 1752 - 1769 (2021)

Pereira, J.; Simpkin, A.; Hartmann, M.; Rigden, D.; Keegan, R.; Lupas, A.: High-accuracy protein structure prediction in CASP14. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), 2020-05 - 2020-09. Proteins: Structure, Function, and Bioinformatics 89 (12), pp. 1687 - 1699 (2021)

Pereira, J.; Lupas, A.: Motif amplification and fold change: explaining the bacterial origin of mitochondria-specific outer membrane β-barrels. In Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2019), p. 26. Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2019), Lisboa, Portugal, December 20, 2019. (2019)

Pereira, J.; Rau, A.; Coles, M.; ElGamacy, M.; Fujishima, K.; Martin, J.; Lupas, A.: The KH type III domain: From an ancestral peptide to three different protein folds. In Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2018), K4, pp. 7 - 8. Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2018), Porto, Portugal, December 21, 2018. (2018)

Alva, V.; Zhu, H.; Hartmann, M.; Pereira, J.; Springer, F.; Martin, J.; Lupas, A.: Ribosomal proteins as documents of the transition from unstructured polypeptides to folded proteins. In CAS Conference 2018: Molecular Origins of LIFE, p. 19. CAS Conference 2018: Molecular Origins of LIFE, München, Germany, October 11, 2018 - October 12, 2018. (2018)

Chojnowski, G.; Pereira, J.; Heuser, P.; Lamzin, V.: Building atomic models into electron-microscopy maps with ARP/wARP. In 26th Annual Meeting of the German Crystallographic Society (DGK 2018). 26th Annual Meeting of the German Crystallographic Society (DGK 2018), Essen, Germany, March 05, 2018 - March 08, 2018. (2018)

Pereira, J.: How do i get the most out of my sequence? Sequence annotation for downstream experiment design. CCP4 Virtual Study Weekend (2022)

Pereira, J.; Lupas, A.: On the origins of the protein world: A large-scale computational approach to study the emergence of the first autonomously folding proteins. The Molecular Origins of Life Conference 2020, München, Germany (2020)

Pereira, J.; Lupas, A.: On the origins of the protein world: a computational approach to study the emergence of the first autonomously folding proteins. CAS Conference 2018: Molecular Origins of LIFE (MOM 2018), München, Germany (2018)

Topitsch, A.; Schwede, T.; Pereira, J.: Outer membrane beta-barrel structure prediction through the lens of AlphaFold2. (submitted)