biorxiv
2026
Diagnosing protein sequence search in the era of language models
Zhou, H., Yang, Y., Lu, Y. Y.
benchmark-datasetprotein-language-modelhybrid-computationalcomputational-onlygeneral
biorxiv
2026
CombinGym: a benchmark platform for machine learning-assisted design of combinatorial protein variants
Chen, Y., Fu, L., Lu, X., Li, W., Gao, Y., Wang, Y., Ruan, Z., Si, T.
function-predictionsubstrate-specificitybenchmark-datasetbayesian-optimizationcomputational-onlygeneral
biorxiv
2026
Benchmarking and Experimental Validation of Machine Learning Strategies for Enzyme Engineering
Zeng, Z., Jin, J., Xu, R., Luo, X.
enzyme-designstability-expressiondirected-evolutionbenchmark-datasethybrid-computationalcomputational-onlygeneral
biorxiv
2026
Protenix-v2: Broadening the Reach of Structure Prediction and Biomolecular Design
Zhang, Y., Gong, C., Sun, J., Guan, J., Ren, M., Xue, S., Zhang, H., Ma, W., Liu, Z., Chen, X., Xiao, W.
enzyme-designbayesian-optimizationcomputational-onlygeneral
Nature Communications
2026
Accelerated discovery of highly active enzyme nanohybrids with parallelized Bayesian optimization in hybrid space
Yu Liu, Haoyang Hu, Yueheng Han, Jia Song Deon Chon, Chin Lee Lo, Zhixuan Chen, Zheng Zhang, Zhihong Yuan, Jun Ge
enzyme-designbayesian-optimizationcomputational-onlygeneral
biorxiv
2026
Characterization of selective pressures acting on protein sites with Deep Learning
Bergiron, E., Nesterenko, L., Barnier, J., Veber, P., Boussau, B.
benchmark-datasethybrid-computationalcomputational-onlygeneral
biorxiv
2026
Additive baselines furnish no evidence for epistasis learning by MULTI-evolve
Visani, G. M., Verma, A., DeWitt, W. S.
benchmark-datasetprotein-language-modelcomputational-onlygeneral
biorxiv
2026
Beyond Structure and Affinity: Context-Dependent Signals for de novo Binder Success
Bozkurt, C.
stability-expressionbenchmark-datasetbayesian-optimizationcomputational-onlygeneral
