Yang, Kevin K.

Protein structure generation via folding diffusion

Wu, K. E., Yang, K. K., Berg, R. V. D., Zou, J. Y., Lu, A. X., & Amini, A. P. (2022) · arXiv

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 193

Protein generation with evolutionary diffusion: sequence is all you need

Alamdari, S., Thakkar, N., van den Berg, R., Tenenholtz, N., Strome, R., Moses, A. M., Lu, A. X., Fusi, N., Amini, A. P., & Yang, K. K. (2023) · eLife

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 154

Convolutions are competitive with transformers for protein sequence pretraining

Yang, K. K., Fusi, N., & Lu, A. X. (2024) · Cell Systems

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 137

Machine learning modeling of family wide enzyme-substrate specificity screens

Goldman, S., Das, R., Yang, K. K., & Coley, C. W. (2022) · PLOS Computational Biology

Computational Drug Discovery MethodsMachine Learning in Bioinformatics

Cited by 120

Masked Inverse Folding with Sequence Transfer for Protein Representation Learning

Yang, K. K., Yeh, H., & Zanichelli, N. (2022) · Protein Engineering Design and Selection

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 110

Computational scoring and experimental evaluation of enzymes generated by neural networks

Johnson, S. R., Fu, X., Viknander, S., Goldin, C., Monaco, S., Zelezniak, A., & Yang, K. K. (2025) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 99

iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode

Wang, J., Youkharibache, P., Marchler-Bauer, A., Lanczycki, C., Zhang, D., Lu, S., Madej, T., Marchler, G. H., Cheng, T., Chong, L. C., et al. (2022) · Frontiers in Molecular Biosciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 65

iCn3D: From Web-based 3D Viewer to Structural Analysis Tool in Batch Mode

Wang, J., Youkharibache, P., Marchler-Bauer, A., Lanczycki, C., Zhang, D., Lu, S., Madej, T., Marchler, G. H., Cheng, T., Chong, L. C., et al. (2021) · Frontiers in Molecular Biosciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 65

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models

Li, F.-Z., Amini, A. P., Yue, Y., Yang, K. K., & Lu, A. X. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 51

Democratizing protein language model training, sharing and collaboration

Su, J., Li, Z., Tao, T., Han, C., He, Y., Dai, F., Yuan, Q., Gao, Y., Si, T., Zhang, X., et al. (2026) · Nature Biotechnology

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 35

Deep learning guided design of protease substrates

Martin-Alonso, C., Alamdari, S., Samad, T. S., Yang, K. K., Bhatia, S. N., & Amini, A. P. (2026) · Nature Communications

Protease and Inhibitor MechanismsComputational Drug Discovery Methods

Cited by 14

Deep learning guided design of protease substrates

Martin-Alonso, C., Alamdari, S., Samad, T. S., Yang, K. K., Bhatia, S. N., & Amini, A. P. (2025) · Nature Communications

Protease and Inhibitor MechanismsComputational Drug Discovery Methods

Cited by 13