Orengo, Christine

The InterPro protein families and domains database: 20 years on

Blum, M., Chang, H.-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., et al. (2021) · Nucleic Acids Research

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 2,231

InterPro: the integrative protein signature database

Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., et al. (2009) · Nucleic Acids Research

Genomics and Phylogenetic StudiesBioinformatics and Genomic Networks

Cited by 2,107

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P., Bridge, A., Brown, S. D., Chang, H.-Y., El-Gebali, S., Fraser, M. I., et al. (2019) · Nucleic Acids Research

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 1,426

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods

Bioinformatics and Genomic NetworksMachine Learning in Bioinformatics

Cited by 1,028

CATH: increased structural coverage of functional space

Sillitoe, I., Bordin, N., Dawson, N., Waman, V. P., Ashford, P., Scholes, H. M., Pang, C. S. M., Woodridge, L., Rauer, C., Sen, N., et al. (2021) · Nucleic Acids Research

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 509

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 452

Exploring structural diversity across the protein universe with The Encyclopedia of Domains

Lau, A. M., Bordin, N., Kandathil, S. M., Sillitoe, I., Waman, V. P., Wells, J., Orengo, C. A., & Jones, D. T. (2024) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 140

Exploring structural diversity across the protein universe with The Encyclopedia of Domains

Lau, A. M., Bordin, N., Kandathil, S. M., Sillitoe, I., Waman, V. P., Wells, J., Orengo, C. A., & Jones, D. T. (2024) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 140

Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)

Ranea, J. A. G., Sillero, A., Thornton, J. M., & Orengo, C. A. (2006) · Journal of Molecular Evolution

Genomics and Phylogenetic StudiesOrigins and Evolution of Life

Cited by 122

Contrastive learning on protein embeddings enlightens midnight zone

Heinzinger, M., Littmann, M., Sillitoe, I., Bordin, N., Orengo, C., & Rost, B. (2021) · NAR Genomics and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 105

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Bordin, N., Sillitoe, I., Nallapareddy, V., Rauer, C., Lam, S. D., Waman, V. P., Sen, N., Heinzinger, M., Littmann, M., Kim, S., et al. (2022) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 103

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Bordin, N., Sillitoe, I., Nallapareddy, V., Rauer, C., Lam, S. D., Waman, V. P., Sen, N., Heinzinger, M., Littmann, M., Kim, S., et al. (2023) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 103

PDBe-KB: collaboratively defining the biological context of structural data

PDBe-KB consortium, Varadi, M., Anyango, S., Armstrong, D., Berrisford, J., Choudhary, P., Deshpande, M., Nadzirin, N., Nair, S. S., Pravda, L., et al. (2022) · Nucleic Acids Research

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 82

Novel machine learning approaches revolutionize protein knowledge

Bordin, N., Dallago, C., Heinzinger, M., Kim, S., Littmann, M., Rauer, C., Steinegger, M., Rost, B., & Orengo, C. (2023) · Trends in Biochemical Sciences

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 72

Chainsaw: protein domain segmentation with fully convolutional neural networks

Wells, J., Hawkins-Hooker, A., Bordin, N., Sillitoe, I., Paige, B., & Orengo, C. (2023) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 53

Chainsaw: protein domain segmentation with fully convolutional neural networks

Wells, J., Hawkins-Hooker, A., Bordin, N., Sillitoe, I., Paige, B., & Orengo, C. (2024) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 53

CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models

Nallapareddy, V., Bordin, N., Sillitoe, I., Heinzinger, M., Littmann, M., Waman, V. P., Sen, N., Rost, B., & Orengo, C. (2023) · Bioinformatics

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 47

Enhancing missense variant pathogenicity prediction with protein language models using VariPred

Lin, W., Wells, J., Wang, Z., Orengo, C., & Martin, A. C. R. (2024) · Scientific Reports

Genomics and Rare DiseasesMachine Learning in Bioinformatics

Cited by 34

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · GigaScience

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 32

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors

Varadi, M., Bordin, N., Orengo, C., & Velankar, S. (2023) · Current Opinion in Structural Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 29

Dissecting peripheral protein-membrane interfaces

Tubiana, T., Sillitoe, I., Orengo, C., & Reuter, N. (2022) · PLoS Computational Biology

Lipid Membrane Structure and BehaviorProtein Structure and Dynamics

Cited by 28

Dissecting peripheral protein-membrane interfaces

Tubiana, T., Sillitoe, I., Orengo, C., & Reuter, N. (2022) · PLOS Computational Biology

Lipid Membrane Structure and BehaviorProtein Structure and Dynamics

Cited by 28

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

Vallat, B., Tauriello, G., Bienert, S., Haas, J., Webb, B. M., Žídek, A., Zheng, W., Peisach, E., Piehl, D. W., Anischanka, I., et al. (2023) · Journal of Molecular Biology

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 26

Characterizing and explaining impact of disease-associated mutations in proteins without known structures or structural homologues

Sen, N., Anishchenko, I., Bordin, N., Sillitoe, I., Velankar, S., Baker, D., & Orengo, C. (2021) · Briefings in Bioinformatics

Protein Structure and DynamicsGenomics and Rare Diseases

Cited by 25