• 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.

Prediction

The web server provides fast pKa calculations of Asp, Glu, His and Lys residues in a protein. Entering a valid PDB code or uploading a PDB format file is required to submit a job.

Tip

The present version is designed to record the results of latest 20 jobs submitted with PDB codes and the results can be traced from HISTORY RUN page.

Input

Input Type

PDB ID

PDB File

PDB Batch Calculation

Submit

pKa Database

    PHMD630

    CpHMD calculated pKa values of 33904 Asp, Glu, His and Lys residues in 630 proteins.

    EXP103S

    Experimental pKa values of 284 Asp, Glu, His and Lys residues in 87 proteins.

    PHMD549 & EXP67S

    Previous CpHMD calculated 26552 pKa's in 549 proteins and experimental 167 pKa's in 52 proteins.

    DeepKa Database

    DeepKa calculated pKa values of 14 M Asp, Glu, His and Lys residues in 150 K proteins.

    Developers

    Zhitao Cai, B.S.

    Jimei University

    Xiangxiang Lu, M.S.

    Jimei University

    Jiawen Sun, B.S.

    Jimei University

    Yandong Huang, Ph.D.

    Associate Professor

    Jimei University

    Any Questions?

    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