• 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

Submit

Database

pKa datasets PHMD549 and EXP67S below can be utilized to establish and test a protein pKa predictor, respectively.

EXP67S

Experimental pKa values of 167 Asp, Glu, His and Lys residues.

PHMD549

Calculated pKa values of 26552 Asp, Glu, His and Lys residues.

Developers

Zhitao Cai, B.S.

Jimei University

Hao Peng, B.S.

Jimei University

Yandong Huang, Ph.D.

Associate Professor

Jimei University

Any Questions?

Please cite the following three references in publications:

[1] Cai, Z.; Peng, H.; Sun, S.; He, J.; Luo, F.; Huang, Y.* DeepKa Web Server: High-Throughput 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