2017

26.Crystal structures of agonist-bound human cannabinoid receptor CB1.

Hua, T.; Vemuri, K.; Nikas, S.; Laprairie, R. B.; Wu, Y.; Qu, L.; Pu, M.; Korde, A.; Shan J.; Ho, J. H.; Han, G. W.; Ding, K.; Li X.; Liu H.; Hanson, M. A.; Zhao, S.*; Bohn, L. M.*; Makriyannis, A.*; Stevens, R. C.; Liu, Z. J.*, Crystal structures of agonist-bound human cannabinoid receptor CB1. Nature. 2017 Jul 5. doi: 10.1038/nature23272.[Membrane Protein]

25.A Novel Lid-Covering Peptide Inhibitor of Nicotinic Acetylcholine Receptors Derived from αD-Conotoxin GeXXA.

Yang, L.; Tae, H.-S.; Fan, Z.; Shao, X.; Xu, S.; Zhao, S.; Adams, D.; Wang, C., A Novel Lid-Covering Peptide Inhibitor of Nicotinic Acetylcholine Receptors Derived from αD-Conotoxin GeXXA. Mar Drugs. 2017 Jun 5;15(6).pii:E164.[Membrane Protein]

24.Structural Basis for Apelin Control of the Human Apelin Receptor.

Ma, Y.; Yue, Y.; Ma, Y.; Zhang, Q.; Zhou, Q.; Song, Y.; Shen, Y.; Li, X.; Ma, X.; Li, C.; Hanson, M. A.; Han, G. W.; Sickmier, E. A.; Swaminath, G.; Zhao, S.; Stevens, R. C.; Hu, L. A.; Zhong, W.; Zhang, M.; Xu, F., Structural Basis for Apelin Control of the Human Apelin Receptor. Structure. 2017 Jun 6;25(6):858-866.[Membrane Protein]

23.Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators.

Song, G.; Yang, D.; Wang, Y.; de Graaf, C.; Zhou, Q.; Jiang, S.; Liu, K.; Cai, X.; Dai, A.; Lin, G.; Liu, D.; Wu, F.; Wu, Y.; Zhao, S.; Ye, L.; Han, G. W.; Lau, J.; Wu, B.; Hanson, M. A.; Liu, Z.-J.; Wang, M.-W.; Stevens, R. C., Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators. Nature. 2017 Jun 8;546(7657):312-315.[Membrane Protein]

22.Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand.

Zhang, X.; Zhao, F.; Wu, Y.; Yang, J.; Han, G. W.; Zhao, S.; Ishchenko, A.; Ye, L.; Lin, X.; Ding, K.; Dharmarajan, V.; Griffin, P. R.; Gati, C.; Nelson, G.; Hunter, M. S.; Hanson, M. A.; Cherezov, V.; Stevens, R. C.; Tan, W.; Tao, H.; Xu, F., Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Nat Commun. 2017 May 17;8:15383.[Membrane Protein]

21.A structurally guided dissection-then-evolution strategy for ligand optimization of smoothened receptor.

Ye, L.;Ding, K.; Zhao, F.; Liu, X.; Wu, Y.; Liu, Y.; Xue, D.; Zhou, F.; Zhang, X.; Stevens, R. C.; Xu, F.; Zhao, S.*; Tao, H.*, A structurally guided dissection-then-evolution strategy for ligand optimization of smoothened receptor. Med. Chem. Commun. 2017,8, 1332-1336.[Membrane Protein]

20.Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space.

Zhou, Q.; Sun, X.; Xia, X.; Fan, Z.; Luo, Z.; Zhao, S.; Shakhnovich, E.; Liang, H., Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space. J Phys Chem Lett. 2017 Jan 19;8(2):407-414.

2016

19.Crystal Structure of the Human Cannabinoid Receptor CB1.

Hua, T.; Vemuri, K.; Pu, M.; Qu, L.; Han, G. W.; Wu, Y.; Zhao, S.; Shui, W.; Li, S.; Korde, A.; Laprairie, R. B.; Stahl, E. L.; Ho, J. H.; Zvonok, N.; Zhou, H.; Kufareva, I.; Wu, B.; Zhao, Q.; Hanson, M. A.; Bohn, L. M.; Makriyannis, A.; Stevens, R. C.; Liu, Z. J., Crystal Structure of the Human Cannabinoid Receptor CB1. Cell. 2016 Oct 20;167(3):750-762.[Membrane Protein]

18.Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.

Zhang, X. S.; Carter, M. S.; Vetting, M. W.; Francisco, B. S.; Zhao, S. W.; Al-Obaidi, N. F.; Solbiati, J. O.; Thiaville, J. J.; de Crecy-Lagard, V.; Jacobson, M. P.; Almo, S. C.; Gerlt, J. A., Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4161-9.[Pathway Docking and Genome Mining]

2015

17.Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

Vetting, M. W.; Al-Obaidi, N.; Zhao, S.; San Francisco, B.; Kim, J.; Wichelecki, D. J.; Bouvier, J. T.; Solbiati, J. O.; Vu, H.; Zhang, X.; Rodionov, D. A.; Love, J. D.; Hillerich, B. S.; Seidel, R. D.; Quinn, R. J.; Osterman, A. L.; Cronan, J. E.; Jacobson, M. P.; Gerlt, J. A.; Almo, S. C., Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 2015 Jan 27;54(3):909-31.[Pathway Docking and Genome Mining]

16.A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily.

Zhang, X.; Kumar, R.; Vetting, M. W.; Zhao, S.; Jacobson, M. P.; Almo, S. C.; Gerlt, J. A., A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. J Am Chem Soc. 2015 Feb 4;137(4):1388-91.[Pathway Docking and Genome Mining]

2014

15.Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.

Jacobson, M. P.; Kalyanaraman, C.; Zhao, S.; Tian, B., Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci. 2014 Aug;39(8):363-71.[Pathway Docking and Genome Mining]

14.Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.

Zhao, S.; Sakai, A.; Zhang, X.; Vetting, M. W.; Kumar, R.; Hillerich, B.; San Francisco, B.; Solbiati, J.; Steves, A.; Brown, S.; Akiva, E.; Barber, A.; Seidel, R. D.; Babbitt, P. C.; Almo, S. C.; Gerlt, J. A.; Jacobson, M. P., Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30;3.[Pathway Docking and Genome Mining]

13.Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.

Kumar, R.;Zhao, S.; Vetting, M. W.; Wood, B. M.; Sakai, A.; Cho, K.; Solbiati, J.; Almo, S. C.; Sweedler, J. V.; Jacobson, M. P.; Gerlt, J. A.; Cronan, J. E., Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio. 2014 Feb 11;5(1):e00933-13.[Pathway Docking and Genome Mining]

2013

12.Discovery of new enzymes and metabolic pathways by using structure and genome context.

Zhao, S. W.; Kumar, R.; Sakai, A.; Vetting, M. W.; Wood, B. M.; Brown, S.; Bonanno, J. B.; Hillerich, B. S.; Seidel, R. D.; Babbitt, P. C.; Almo, S. C.; Sweedler, J. V.; Gerlt, J. A.; Cronan, J. E.; Jacobson, M. P., Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Oct 31;502(7473):698-702.[Pathway Docking and Genome Mining]

11.Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.

Tian, B.; Wallrapp, F.; Kalyanaraman, C.; Zhao, S.; Eriksson, L. A.; Jacobson, M. P., Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase. Biochemistry. 2013 Aug 20;52(33):5511-3.

10.Prediction of Long Loops with Embedded Secondary Structure Using the Protein Local Optimization Program.

Miller, E. B.; Murrett, C. S.; Zhu, K.; Zhao, S. W.; Goldfeld, D. A.; Bylund, J. H.; Friesner, R. A., Prediction of Long Loops with Embedded Secondary Structure Using the Protein Local Optimization Program. J Chem Theory Comput. 2013 Mar 12;9(3):1846-4864.

2011

9.The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling.

Li, J.; Abel, R.; Zhu, K.; Cao, Y.; Zhao, S.; Friesner, R. A., The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins. 2011 Oct;79(10):2794-812.

8.Progress in super long loop prediction.

Zhao, S.; Zhu, K.; Li, J.; Friesner, R. A., Progress in super long loop prediction. Proteins. 2011 Oct;79(10):2920-35.

2008

7.Toward better refinement of comparative models: predicting loops in inexact environments.

Sellers, B. D.; Zhu, K.; Zhao, S.; Friesner, R. A.; Jacobson, M. P., Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15;72(3):959-71.

2007

6.Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.

Li, X.; Jacobson, M. P.; Zhu, K.; Zhao, S. W.; Friesner, R. A., Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins. 2007 Mar 1;66(4):824-37.

2006

5.Long loop prediction using the protein local optimization program.

Zhu, K.; Pincus, D. L.; Zhao, S. W.; Friesner, R. A., Long loop prediction using the protein local optimization program. Proteins. 2006 Nov 1;65(2):438-52.

2005

4.Assessment of the metabolic stability of the methyl groups in heterocyclic compounds using C-H bond dissociation energies: Effects of diverse aromatic groups on the stability of methyl radicals.

Zhao, S. W.; Liu, L.; Fu, Y.; Guo, Q.-X., Assessment of the metabolic stability of the methyl groups in heterocyclic compounds using C-H bond dissociation energies: Effects of diverse aromatic groups on the stability of methyl radicals. J Phys Org Chem. 2005, 18 (4), 353-367.

2004

3.Blue-shifted dihydrogen bonds.

Feng, Y.; Zhao, S. W.; Liu, L.; Wang, J. T.; Li, X. S.; Guo, Q. X., Blue-shifted dihydrogen bonds. J Phys Org Chem. 2004, 17 (12), 1099-1106.

2.Origin of conformational restriction in complexes of formyl compounds with boron lewis acids and their related systems.

Feng, Y.; Liu, L.; Zhao, S. W.; Wang, J. T.; Guo, Q. X., Origin of conformational restriction in complexes of formyl compounds with boron lewis acids and their related systems. J. Phys. Chem. A. 2004, 108 (42), pp 9196–9204.

1.Homolytic C-H and N-H bond dissociation energies of strained organic compounds.

Feng, Y.; Liu, L.; Wang, J. T.; Zhao, S. W.; Guo, Q. X., Homolytic C-H and N-H bond dissociation energies of strained organic compounds. J Org Chem. 2004 Apr 30;69(9):3129-38.