Publications

* Senior Author or Co-Senior Author

Wei, Y., Huyghes-Despointes, B. M. P., Tsai, J., and Scholtz, J. M. Simple mutations can dramatically alter the structure and stability of the second hairpin of the B1 domain of protein. (2007) G.Proteins (Accepted) :.
Kim, S., *Tsai, J., Kagiampakis, I., Liwang, P., and Vannucci, M. Detecting protein dissimilarities in multiple alignments using Bayesian variable selection. (2007) Bioinformatics 23:245-6.
Rohl, C., Price, Y., Fischer, T. B., Paczkowski, M., Zettel, M. F., and *Tsai, J. Cataloging the relationships between proteins: a review of interaction databases. (2006) Mol Biotechnol 34:69-93.
Huyghes-Despointes, B.M.P., Qu, X., *Tsai, J., and Scholtz, J.M. Terminal ion pairs stabilize the second beta-hairpin of the B1 domain of protein G. (2006) Proteins 63:1005-17.
Schell, D., Tsai, J., Scholtz, J.M., and Pace, C.N. Hydrogen bonding increases packing density in the protein interior. (2006) Proteins 63:278-82.
Fischer, T.B., Holmes, J.B., Miller, I.R., Parsions, J.R., Tung, L., Hu, J.C., and *Tsai, J. Assessing methods for identifying pair-wise atomic contacts across binding interfaces. (2006) J Struct Biol 153:103-112.
Holmes, J.B., and *Tsai, J. Characterizing conserved structural contacts by pair-wise relative contacts and relative packing groups. (2005) J Mol Biol 354:706-21.
Parsons, J.R., Holmes, J.B., Rojas, J.M., *Tsai, J., and Strauss, C.E. Practical conversion from torsion space to Cartesian space for in silico protein synthesis. (2005) J Comput Chem 26:1063-8.
Fischer, T.B., Paczkowski, M., Zettel, M.F., and *Tsai, J. Will this relationship work? A guide to protein interaction databases. (2005) The Proteomics Protocol Handbook (Walker, J., Ed.), Humana Press, Totowa, NJ.

Holmes, J.B., and *Tsai, J. Some fundamental aspects of building protein structures from fragment libraries. (2004) Protein Sci 13:1636-1650.
Swanson, R., and *Tsai, J. Pretty good guessing: protein structure prediction at CASP5. (2003) J Bacteriol 185:3990-3.
Fischer, T.B., Arunachalam, K.V., Bailey, D., Mangual, V., Bakhru, S., Russo, R., Huang, D., Paczkowski, M., Lalchandani, V., Ramachandra, C., Ellison, B., Galer, S., Shapely, J., Fuentes, E., and *Tsai, J. The Binding Interface Database (BID): a compilation of amino acid hot spots in protein interfaces. (2003) Bioinformatics 19:1453-84.
Krebs, W.G., Tsai, J., Alexandrov, V., Junker, J., Jansen, R., and Gerstein, M. Tools and databases to analyze protein flexibility; Approaches to mapping implied features onto sequences. (2003) Methods Enzymol 374:544-84.
Tsai, J., Bonneau, R., Morozov, A.V., Kuhlman, B., Rohl, C.A., and Baker, D. An improved protein decoy set for testing energy functions for protein structure prediction. (2003) Proteins 53:76-87.
Tsai, J., and Levitt, M. Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G. (2002) Biophys Chem 101-102:187-201.
Bonneau, R., Ruczinski, I., Tsai, J., and Baker, D. Contact order and ab initio protein structure prediction. (2002) Protein Sci 11:1937-44.
Tsai, J., and Gerstein, M. Calculations of protein volumes: sensitivity analysis and parameter database. (2002) Bioinformatics 18:985-95.
Raschke, T.M., Tsai, J., and Levitt, M. Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water. (2001) Proc Natl Acad Sci USA 98:5965-9.
Lee, M.R., Tsai, J., Baker, D., and Kollman, P.A. Molecular dynamics in the endgame of protein structure prediction. (2001) J Mol Biol 313:417-30.
Tsai, J., Voss, N., and Gerstein, M. Determining the minimum number of types necessary to represent the sizes of protein atoms. (2001) Bioinformatics 17:949-56.
Bonneau, R., Tsai, J., Ruczinski, I., Chivian, D., Rohl, C., Strauss, C.E., and Baker, D. Rosetta in CASP4: Progress in ab initio protein structure prediction. (2001) Proteins 45 Suppl 5:119-26.
Bonneau, R., Tsai, J., Ruczinski, I., and Baker, D. Functional inferences from blind ab initio protein structure predictions. (2001) J Struct Biol 134:186-90.
Tsai, J., Taylor, R., Chothia, C., and Gerstein, M. The packing density in proteins: standard radii and volumes. (1999) J Mol Biol 290:253-66.
Tsai, J., Levitt, M., and Baker, D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. (1999) J Mol Biol 291:215-25.
Tsai, J., Gerstein, M., and Levitt, M. Simulating the minimum core for hydrophobic collapse in globular proteins. (1997) Protein Sci 6:2606-16.
Levitt, M., Gerstein, M., Huang, E., Subbiah, S., and *Tsai, J. Protein Folding: The Endgame. (1997) Annu Rev Biochem 66:549-79.
Huang, E.S., Subbiah, S., Tsai, J. and Levitt, M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. (1996) J Mol Biol 257:716-25.
Tsai, J., Gerstein, M., and Levitt, M. Keeping the shape but changing the charges – A simulation study of urea and its iso-static analogues. (1996) J Chem Phys 104:9417-9430.
Gerstein, M., Tsai, J., and Levitt, M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. (1995) J Mol Biol 249:955-66..
Abuladze, N.K., Gingery, M., Tsai, J., and Eiserling, F.A. Tail length determination in bacteriophage T4. (1994) Virology 199:301-10.