Pereira, Joana

High‐accuracy protein structure prediction in CASP14

Pereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M., & Lupas, A. N. (2021) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 314

Assessing the utility of CASP14 models for molecular replacement

Millán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J., & Read, R. J. (2021) · Proteins: Structure, Function, and Bioinformatics

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 62

Embedding-based alignment: combining protein language models and alignment approaches to detect structural similarities in the twilight-zone

Pantolini, L., Studer, G., Pereira, J., Durairaj, J., & Schwede, T. (2022) · Bioinformatics

Machine Learning in BioinformaticsGenomics and Phylogenetic Studies

Cited by 55

Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone

Pantolini, L., Studer, G., Pereira, J., Durairaj, J., Tauriello, G., & Schwede, T. (2024) · Bioinformatics

Machine Learning in BioinformaticsGenomics and Phylogenetic Studies

Cited by 55

Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study

Durairaj, J., Follonier, O. M., Leuzinger, K., Alexander, L. T., Wilhelm, M., Pereira, J., Hillenbrand, C. A., Weissbach, F. H., Schwede, T., & Hirsch, H. H. (2023) · mSphere

Polyomavirus and related diseasesvaccines and immunoinformatics approaches

Cited by 23

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

Odai, R., Leemann, M., Al-Murad, T., Abdullah, M., Shyrokova, L., Tenson, T., Hauryliuk, V., Durairaj, J., Pereira, J., & Atkinson, G. C. (2025) · Science Advances

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 16

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

Odai, R., Leemann, M., Al-Murad, T., Abdullah, M., Shyrokova, L., Tenson, T., Hauryliuk, V., Durairaj, J., Pereira, J., & Atkinson, G. C. (2025) · Science Advances

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 16

Outer membrane β-barrel structure prediction through the lens of AlphaFold2

Topitsch, A., Schwede, T., & Pereira, J. (2022) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 9

Outer membrane β‐barrel structure prediction through the lens of AlphaFold2

Topitsch, A., Schwede, T., & Pereira, J. (2024) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 9

New β-Propellers Are Continuously Amplified From Single Blades in all Major Lineages of the β-Propeller Superfamily

Pereira, J., & Lupas, A. N. (2022) · Frontiers in Molecular Biosciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 8

New β-propellers are continuously amplified from single blades in all major lineages of the β-propeller superfamily

Pereira, J., & Lupas, A. N. (2022) · Frontiers in Molecular Biosciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 8