• Huang Lab

    Our research interests include molecular mechanism of proton-coupled mass transfer across cellular membrane and development of protein pKa predictor.

  • pH and pKa

    pH represents solution acidity and plays a key role in many biological processes via protonation or deprotonation of key ionizable residues in a protein where titration equilibria are determined by pKa values which can be measured typically by NMR or estimated by a theoretical model.

  • About DeepKa

    DeepKa, a deep learning-based protein pKa predictor, is built based on pKa's calculated by continuous constant pH molecular dynamics simulations.

DeepKa Database

Soluble proteins in PDB

pKa values of 30873399 Asp, Glu, His and Lys residues in 197148 soluble proteins.

Membrane proteins in OPM

pKa values of 1984563 Asp, Glu, His and Lys residues in 8711 transmembrane proteins.

Soluble proteins in PDBbind

pKa values of 2367154 Asp, Glu, His and Lys residues in 23337 protein-nucleic acid (PN), protein-protein (PP),and protein-ligand (PL_refined and PL_other) complexes.

Please cite the following references in publications:

[1] Cai, Z.; Peng, H.; Sun, S.; He, J.; Luo, F.; Huang, Y.* DeepKa Web Server: High-Throughput Protein pKa Prediction. Journal of Chemical Information and modeling (2024) 64:2933-2940

[2] Cai, Z.; Liu, T.; Lin, Q.; He, J.; Lei, X.; Luo, F.; Huang, Y.* Basis for accurate protein pKa prediction with machine learning.
Journal of Chemical Information and modeling (2023) 63:2936-2947

[3] Cai, Z.; Luo, F.; Wang, Y.; Li, E.; Huang, Y.* Protein pKa prediction with machine learning. ACS Omega (2021) 6:34823-34831