Anishchenko, Ivan

Accurate prediction of protein structures and interactions using a 3-track network

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 5,549

Robust deep learning–based protein sequence design using ProteinMPNN

Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,210

Robust deep learning based protein sequence design using ProteinMPNN

Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,107

Improved protein structure prediction using predicted interresidue orientations

Yang, J., Anishchenko, I., Park, H., Peng, Z., Ovchinnikov, S., & Baker, D. (2020) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 1,421

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Krishna, R., Wang, J., Ahern, W., Sturmfels, P., Venkatesh, P., Kalvet, I., Lee, G. R., Morey-Burrows, F. S., Anishchenko, I., Humphreys, I. R., et al. (2024) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 978

De novo protein design by deep network hallucination

Anishchenko, I., Chidyausiku, T. M., Ovchinnikov, S., Pellock, S. J., & Baker, D. (2020) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 629

Computed structures of core eukaryotic protein complexes

Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S. R., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 542

Structures of core eukaryotic protein complexes

Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 541

Deep learning methods for designing proteins scaffolding functional sites

Wang, J., Lisanza, S., Juergens, D., Tischer, D., Anishchenko, I., Baek, M., Watson, J. L., Chun, J. H., Milles, L. F., Dauparas, J., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 487

Scaffolding protein functional sites using deep learning

Wang, J., Lisanza, S., Juergens, D., Tischer, D., Watson, J. L., Castro, K. M., Ragotte, R., Saragovi, A., Milles, L. F., Baek, M., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 487

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

Baek, M., McHugh, R., Anishchenko, I., Jiang, H., Baker, D., & DiMaio, F. (2024) · Nature Methods

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 372

Improved protein structure refinement guided by deep learning based accuracy estimation

Hiranuma, N., Park, H., Baek, M., Anishchenko, I., Dauparas, J., & Baker, D. (2021) · Nature Communications

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 243

Protein interaction networks revealed by proteome coevolution

Cong, Q., Anishchenko, I., Ovchinnikov, S., & Baker, D. (2019) · Science

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 241

Computational design of serine hydrolases

Lauko, A., Pellock, S. J., Sumida, K. H., Anishchenko, I., Juergens, D., Ahern, W., Jeung, J., Shida, A. F., Hunt, A., Kalvet, I., et al. (2025) · Science

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 235

Origins of coevolution between residues distant in protein 3D structures

Anishchenko, I., Ovchinnikov, S., Kamisetty, H., & Baker, D. (2017) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 185

Protein sequence design by conformational landscape optimization

Norn, C., Wicky, B. I. M., Juergens, D., Liu, S., Kim, D., Tischer, D., Koepnick, B., Anishchenko, I., Players, F., Baker, D., et al. (2021) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 144

Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

Krishna, R., Wang, J., Ahern, W., Sturmfels, P., Venkatesh, P., Kalvet, I., Lee, G. R., Morey-Burrows, F. S., Anishchenko, I., Humphreys, I. R., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 106

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

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

Protein oligomer modeling guided by predicted interchain contacts in CASP14

Baek, M., Anishchenko, I., Park, H., Humphreys, I. R., & Baker, D. (2021) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 18