Howook Hwang

Howook Hwang


Senior Computational Scientist

As a senior computational scientist in the Honig Lab, Howook Hwang is investigating and developing computational algorithms for using protein structure to predict protein-protein and protein-small ligand interactions on a genome-wide scale. His approach integrates cutting edge template-based methods and empirical score based methods using various machine learning techniques including Bayesian network methods to analyze large collections of biological data and elucidate interaction specificities among the molecules. Dr. Hwang earned his PhD in bioinformatics working in Zhiping Weng’s lab at Boston University (Dr. Weng has since moved to Umass Medical School.) For his thesis he developed algorithms and a database for predicting protein-protein binding activity.

Education History

PhD, Boston University Bioinformatics

BA, George Mason University Computer Science


* Indicates authors contributed equally


Hwang, H., Dey F., Petrey D., Honig. B. Structure-based prediction of ligand-protein interactions on a genome-wide scale. Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13685-13690. doi: 10.1073/pnas.1705381114.  

Hwang H ., Petrey D., Honig B. A Hybrid Method for Protein-protein Interface Prediction Protein . Science, 2016 Jan;25 (1):159-165.

Petrey D, Chen TS, Deng L, Garzon JI, Hwang H , Lasso G, Lee H, Silkov A, Honig B. Template-based prediction of protein function. Curr Opin Struct Biol. 2015 Feb 9;32C:33-38.  

Hwang H , Vreven T, Weng Z. Binding interface prediction by combining protein-protein docking results . Proteins. 2014 Jan;82(1):57-66. 

Pierce BG, Wiehe K, Hwang H , Kim BH, Vreven T, Weng Z. ZDOCK server: integrative docking pediction of protein-protein complexes and symmetric multimers . Bioinformatics. 2014 Jun 15;30(12):1771-3. 

Vreven T*, Hwang H* , Pierce BG, Weng Z. E valuating template-based and template-free protein-protein structure prediction. Brief Bioinform. 2014 Mar;15(2):169-76. 

Moretti R, …, Hwang H , Weng Z, …, Baker D. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions . Proteins. 2013 Nov;81(11):1980-7.

Lensink MF, …, Hwang H , …, Weng Z, …, Wodok SJ. Blind prediction of interfacial water positions in CAPRI . Proteins. 2014 Apr;82(4):620-32.

Vreven T, Pierce BG, Hwang H , Weng Z. Performance of ZDOCK in CAPRI rounds 20-26 . Proteins. 2013 Oct 3.  

Vreven T, Hwang H , Weng Z. Exploring angular distances in protein-protein docking algorithms . PLoS One. 2013;8(2):e56645. 

Vreven T, Hwang H , Pierce BG, Weng Z. Prediction of protein-protein binding free energies . Protein Sci. 2012 Mar;21(3):396-404. 

Vreven T, Hwang H , Weng Z. Integrating atom-based and residue-based scoring functions for protein-protein docking . Protein Sci. 2011 Sep;20(9):1576-86. 

Fleishman SJ, …, Hwang H , Weng Z, …, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology . J Mol Biol. 2011 Nov 25;414(2):289-302. 

Hwang H , Vreven T, Whitfield TW, Wiehe K, Weng Z. A machine learning approach for the prediction of protein surface loop flexibility . Proteins. 2011 Aug;79(8):2467-74. 

Kastritis PL, Moal IH, Hwang H , Weng Z, Bates PA, Bonvin AM, Janin J. A structure-based benchmark for protein-protein binding affinity . Protein Sci. 2011 Mar;20(3):482-91. '

Hwang H , Vreven T, Pierce BG, Hung JH, Weng Z. Performance of ZDOCK and ZRANK in CAPRI round 13-19 . Proteins. 2010 Nov 15;78(15):3104-10. 

Hwang H , Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0 . Proteins. 2010 Nov 15;78(15):3111-4. 

Hwang H , Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0 . Proteins. 2008 Nov 15;73(3):705-9. 

Wiehe K, Pierce B, Tong WW, Hwang H , Mintseris J, Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI . Proteins. 2007 Dec 1;69(4):719-25. 

Hwang H , Pierce B, Weng Z. Protein-protein docking. In: Computational protein-protein interactions. Nussinov R, Schreiber G, eds. Boca Raton, FL: CRC Press. 2009.