Velankar, Sameer

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 7,850

Highly accurate protein structure prediction for the human proteome

Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 3,025

AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

Varadi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2,052

Protein Data Bank: the single global archive for 3D macromolecular structure data

wwPDB consortium, Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C., Duarte, J. M., Dutta, S., et al. (2019) · Nucleic Acids Research

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 1,163

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Sehnal, D., Bittrich, S., Deshpande, M., Svobodová, R., Berka, K., Bazgier, V., Velankar, S., Burley, S. K., Koča, J., & Rose, A. S. (2021) · Nucleic Acids Research

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 1,154

A structural biology community assessment of AlphaFold2 applications

Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 675

Clustering predicted structures at the scale of the known protein universe

Barrio-Hernandez, I., Yeo, J., Jänes, J., Mirdita, M., Gilchrist, C. L. M., Wein, T., Varadi, M., Velankar, S., Beltrao, P., & Steinegger, M. (2023) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 362

Clustering predicted structures at the scale of the known protein universe

Steinegger, M., Beltrao, P., Velankar, S., Varadi, M., Wein, T., Gilchrist, C., Mirdita, M., Jänes, J., Yeo, J., & Barrio-Hernandez, I. (2023) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 362

Clustering predicted structures at the scale of the known protein universe

Barrio-Hernandez, I., Yeo, J., Jänes, J., Wein, T., Varadi, M., Velankar, S., Beltrao, P., & Steinegger, M. (2023) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 362

Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition

Lensink, M. F., Velankar, S., & Wodak, S. J. (2017) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 222

A structural biology community assessment of AlphaFold 2 applications

Akdel, M., Pires, D. E. V., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 122

Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment

Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., et al. (2019) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 122

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

Challenges in bridging the gap between protein structure prediction and functional interpretation

Varadi, M., Tsenkov, M., & Velankar, S. (2025) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 36

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

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

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

Sen, N., Anishchenko, I., Bordin, N., Sillitoe, I., Velankar, S., Baker, D., & Orengo, C. (2022) · Briefings in Bioinformatics

Protein Structure and DynamicsGenomics and Rare Diseases

Cited by 25

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) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2