Kundrotas, Petras

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

Towards a structurally resolved human protein interaction network

Burke, D. F., Bryant, P., Barrio-Hernandez, I., Memon, D., Pozzati, G., Shenoy, A., Zhu, W., Dunham, A. S., Albanese, P., Keller, A., et al. (2023) · Nature Structural & Molecular Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 269

Towards a structurally resolved human protein interaction network

Elofsson, A., Burke, D., Bryant, P., Barrio-Hernandez, I., Memon, D., Pozzati, G., Shenoy, A., Zhu, W., Dunham, A., Albanese, P., et al. (2021) · Nature Structural & Molecular Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 269

Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

Bryant, P., Pozzati, G., Zhu, W., Shenoy, A., Kundrotas, P., & Elofsson, A. (2022) · Nature Communications

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 226

Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.

Elofsson, A., Bryant, P., Pozzati, G., Zhu, W., Shenoy, A., & Kundrotas, P. (2022) · Nature Communications

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 226

Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes

Zhu, W., Shenoy, A., Kundrotas, P., & Elofsson, A. (2023) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 202

Templates are available to model nearly all complexes of structurally characterized proteins

Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A. (2012) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 179

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

Natural language processing in text mining for structural modeling of protein complexes

Badal, V. D., Kundrotas, P. J., & Vakser, I. A. (2018) · BMC Bioinformatics

Biomedical Text Mining and OntologiesProtein Structure and Dynamics

Cited by 34

Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

Anishchenko, I., Kundrotas, P. J., & Vakser, I. A. (2018) · Biophysical Journal

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 29

Limits and potential of combined folding and docking

Pozzati, G., Zhu, W., Bassot, C., Lamb, J., Kundrotas, P., & Elofsson, A. (2022) · Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 25

Computational feasibility of an exhaustive search of side-chain conformations in protein-protein docking

Dauzhenka, T., Kundrotas, P. J., & Vakser, I. A. (2018) · Journal of Computational Chemistry

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 17

How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking

Chakravarty, D., McElfresh, G., Kundrotas, P. J., & Vakser, I. A. (2020) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 13