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Research Interests:

Computational Biology, Bioinformatics, Computer-aided Drug Design (CADD), Chemoinformatics

 

Research Experience and Accomplishments:

Developed several theoretical methods for studying protein/protein interactions, and systematically studied the protein/protein interaction networks mediated by the SH3 modular domains; developed a number of methods, databases and programs for ADME predictions and drug design, which have been widely used by international pharmaceutical companies. More than 110 publications in SCI-cited journals with ~1000 citations (H-index = 20), and contributions to 4 books and 1 multimedia textbook. In 2008, Dr. Hou was awarded the Science and Technology Advancement Award of Chinese Universities (Second Class, rank 2). Dr. Hou is now serving the editorial board or the advisory editorial board in a number of important international journals, including Theoretical Biology & Medical Modelling, Current Pharmaceutical Design, Mini-Reviews in Medicinal Chemistry, Current Computer-aided Drug Design and Medicinal Chemistry.

 

Research group homepage: http://sites.google.com/site/houtingjun


Invited reviews

1. Xinliang Mao*, Tingjun Hou*, Biyin Cao, Fangliang Gan, Depei Wu, Zixing Chen, Exploring old drugs for the treatment of hematological malignancies, Current Medicinal Chemistry, in press.

2. Tingjun Hou*, Junmei Wang, Youyong Li*, Recent progress of in silico predictions of oral bioavailability, Combinatorial Chemistry & High Throughput Screening, in press.

3.   Junmei Wang, Tingjun Hou, Advances of computational predictions of solubility, Combinatorial Chemistry & High Throughput Screening, in press.

4. Youyong Li, Tingjun Hou, Computational simulation of drug delivery at molecular level, Current Medicinal Chemistry, 2010, 17, 4482-4491.

5. Youyong Li, Tingjun Hou*, William A. Goddard III*, Molecular modeling of structure-function of G Protein-Coupled Receptors with applications for drug design, Current Medicinal Chemistry, 2010, 17, 1167-1180.

6. Tingjun Hou*, Yongyong Li, Wei Zhang, Junmei Wang, In silico predictions of intestinal absorption and bioavailability, Combinatorial Chemistry & High Throughput Screening, 2009, 12, 497-506.

7. Tingjun Hou*, Junmei Wang, Structure–ADME relationship: still a long way to go? Expert Opinion on Drug Metabolism and Toxicology, 2009, 4, 759-771.

8. Tingjun Hou, Junmei Wang, Wei Zhang, Wei Wang, Xiaojie Xu, Recent advances in computational prediction of drug absorption and permeability in drug discovery, Current Medicinal Chemistry, 2006, 13, 2653-2667.

9. Junmei Wang, Tingjun Hou, Xiaojie Xu, Recent advances in free energy calculations with a combination of molecular mechanics and continuum models, Current Computer-Aided Drug Design, 2006, 2, 287-306.

10. Tingjun Hou, Xiaojie Xu, Recent development and application of virtual screening in drug discovery: an overview, Current Pharmaceutical Design, 2004, 10, 1011-1033.

 

Selected Publications:

1.   Tingjun Hou*, Junmei Wang, Youyong Li, Wei Wang*, Assessing the performance of the MM/PBSA and MM/GBSA methods: II. The accuracy of ranking poses generated from docking, Journal of Computational Chemistry, in press.

2.   Tingjun Hou*, Junmei Wang, Youyong Li, Wei Wang*, Assessing the performance of the MM/PBSA and MM/GBSA methods: I. The accuracy of binding free energy calculations based on molecular dynamics simulations, Journal of Chemical Information and Modeling, 2011, in press.

3. Yaxue Zhao, Xuefeng Lu, Chaoyie Yang, Zhimin Huang, Tingjun Hou*, Jian Zhang*, Computational modeling toward understanding agonist binding on dopamine 3, Journal of Chemical Information and Modeling, 2010, 50, 1633-1643.

4.   Jing Zhang†, Tingjun Hou† (co-first author), Wei Wang, Jun S. Liu, A Bayesian method for detecting combinatorial mutation patterns responsible for HIV drug resistance, Proceedings of the National Academy of Sciences, 2010, 107, 1321-1326.

(Reported by Science Daily, UCSDNewsCenter and the Harvard Crimson)

5.   Wei Cui, Zhuo, Wei, Quan Chen, Yuanhua Chen, Lingling Geng, Jiang Zhang, Jianhua Chen*, Tingjun Hou*, Mingjuan Ji*, Structure-based design of peptides with cytotoxicity on tumor cells, Journal of Chemical Information and Modeling, 2010, 50, 380-387.

(Cover story)

6.   Tingjun Hou, Zheng Xu, Wei Zhang, William A. McLaughlin, David A. Case, Yang Xu, Wei Wang, Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains, Molecular & Cellular Proteomics, 2009, 8, 639-649.

7. Tingjun Hou, Wei Zhang, Jian Wang, Wei Wang, The prediction of HIV-1 protease drug resistance by analyzing the protease/drug decomposed interaction energy components, Proteins: Structure, Function, and Bioinformatics, 2009, 74, 837-846.

8. Tingjun Hou, Wei Zhang, Case A. David, Wei Wang, Characterization of domain-peptide interaction interface: A case study on the amphiphysis-1 SH3 domain, Journal of Molecular Biology, 2008, 376, 1201-1214.

9. Tingjun Hou, William McLaughlin, Wei Wang, Evaluating the potency of HIV-1 protease drugs to combat resistance, Proteins: Structure, Function, and Bioinformatics, 2008, 71, 1163-1174.

10. Tingjun Hou*, Junmei Wang, Youyong Li, ADME evaluation in drug discovery. 8. The prediction of intestinal absorption by a support vector machine, Journal of Chemical Information and Modeling, 2007, 47, 2408-2415.

11. Tingjun Hou*, Yon Yu, Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance, Journal of Medicinal Chemistry, 2007, 50, 1177-1188.

12. Tingjun Hou*, Junmei Wang, Wei Zhang, Xiaojie Xu, ADME evaluation in drug discovery. 7. Prediction of oral absorption by correlation and classification. Journal of Chemical Information and Modeling, 2007, 47, 208-218. 

(This paper is the 6th most assessed article of JCIM in 2007)

13. Tingjun Hou*, Junmei Wang, Wei Zhang, Xiaojie Xu, ADME evaluation in drug discovery. 6. If the oral bioavailability in human can be effectively predicted by simple molecular properties-based rules? Journal of Chemical Information and Modeling, 2007, 47, 460-463. 

(This paper is the 10th most assessed article of JCIM in 2007)

14. Tingjun Hou, Ken Chen, William McLaughlin, Benzhuo Lu, Wei Wang, Analysis and prediction of peptide binding partners of the Abl SH3 domain. PLoS Computational Biology, 2006, 2, 0046-0055.

(This paper was recommended by Faculty Biology of 1000)

15. Tingjun Hou, William McLaughlin, Benzhuo Lu, Ken Chen, Wei Wang, Prediction of Binding Affinities between the Human Amphiphysin-1 SH3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular dynamics and Molecular Field Analysis. Journal of Proteome Research, 2006, 5, 32-43.

16. Tingjun Hou, Wei Zhang, Ke Xia, Xiaojie Xu, ADME evaluation in drug discovery. 5. Correlation of Caco-2 permeation with simple molecular properties, Journal of Chemical Information and Computer Sciences, 2004, 44, 1585-1600. 

(This paper is the 11th most assessed article of JCICS in 2004)

17. Tingjun Hou, Ke Xia, Wei Zhang, Xiaojie Xu, ADME evaluation in drug discovery. 4. Prediction of aqueous solubility based on atom contribution approach, Journal of Chemical Information and Computer Sciences, 2004, 44, 266-275. 

(This paper is the 10th most assessed article of JCICS in 2004, the reported model was used by MOE)

18. Tingjun Hou, Lili Zhu, Lirong Chen, Xiaojie Xu, Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies, Journal of Chemical Information and Computer Sciences, 2003, 43, 273-287.

19. Tingjun Hou, Xiaojie Xu, ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-additive Approach Based on Atom-weighted Solvent Accessible Surface Areas, Journal of Chemical Information and Computer Sciences, 2003, 43, 1058-1067.

20. Tingjun Hou, Xiaojie Xu, ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors. Journal of Chemical Information and Computer Sciences, 2003, 43, 2137-2152.

21. Tingjun Hou, Xiaojie Xu, Predictions of binding of a diverse set of ligands to gelatinase-A by a combination of molecular dynamics and continuum solvent models, Journal of Physical Chemistry B, 2002, 106, 5527-5535.

22. Tingjun Hou, Xiaojie Xu, Empirical aqueous solvation models based on accessible surface areas with implicit electrostatics, Journal of Physical Chemistry B, 2002, 106, 11295-11304.

23. Tingjun Hou, Xiaojie Xu, Molecular docking simulations of a group of gelatinase-a inhibitors using molecular dynamics, Journal of Computer-aided Molecular Design, 2002, 16, 27-41.

24. Tingjun Hou, Xiaojie Xu, A new molecular simulation software package – Peking University Drug Design System (PKUDDS) for structure-based drug design, Journal of Molecular Graphics and Modeling, 2001, 19, 455-465.

25. Tingjun Hou, Wei Zhang, Xiaojie Xu, Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear response method, Journal of Physical Chemistry B, 2001, 105, 5304-5315.

26. Tingjun Hou, Zhengming Li, Jie Liu, Xiaojie Xu, Three-dimensional quantitative structure activity relationship analysis of the new potent sulfonaylureas using Comparative Molecular Similarity Indices Analysis (CoMSIA), Journal of Chemical Information and Computer Sciences, 2000, 40, 1002-1009.

27. Tingjun Hou, Lili Zhu, Xiaojie Xu, Adsorption and diffusion of benzene in ITQ-1 type zeolite: Grand Canonical Monte Carlo and molecular dynamics simulation study, Journal of Physical Chemistry B, 2000, 104, 9356-9364.

28. Tingjun Hou, Yu An, Binggen Ru, Bi Ruchang, Xiaojie Xu, Cysteine-indepent polymerization of metallothoneins in solutions and crystals, Protein Science, 2000, 9, 2302-2312.

29. Tingjun Hou, Junmei Wang, Xiaojie Xu, Automatic docking of peptides and proteins using a hybrid method combined with genetic algorithm and tabu search, Protein Engineering, 1999, 12, 639-647.

30. Tingjun Hou, Junmei Wang, Ning Liao, Xiaojie Xu, Applications of genetic algorithms on the structure-activity relationships analysis of some cinnamamides, Journal of Chemical Information and Computer Sciences, 1999, 39, 775-781.

 

Book Chapters

1.          Junmei Wang, Tingjun Hou, Recent Advances on in silico ADME Modeling, Annual Reports in Computational Chemistry, Elsevier, Volume 5, 2009, (in press)

2.         Tingjun Hou, Xu Xiaojie, Recent development and application of virtual screening in drug discovery: An Overview. in Frontier in Medicinal Chemistry, Bentham Science Publishers, Vol 3, 2006, 675-703.

3.   Xu Luo, Chemical statistics, Science Publisher, 2002. (Chapter 16)

4.          Xiaojie Xu, Tingjun Hou, Xuebin Qiao, Wei Zhang, Computer-aided drug design: principle, methods and applications, Chemical Industrial Publisher, 2004. (Chapters 4 to 16)

5.          Molecular Conceptor courseware, Synergix Ltd. 2008. (Contributing the chapter: introduction to chemoinformatics).

 

 


 

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