Protein Structure Prediction

Loop modeling: sampling, filtering, and scoring

Proteins-Structure Function and Bioinformatics  2008 70:834-843
Soto, C. S., Fasnacht, M., Zhu, J., Forrest, L., Honig, B.

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

Proteins-Structure Function and Bioinformatics 2008 72:1171-1188
Zhu, J., Fan, H., Periole, X., Honig, B., Mark, A. E.

Local quality assessment in homology models using statistical potentials and support vector machines

Protein Science  2007 16:1557-1568
Fasnacht, M., Zhu, J., Honig, B.

Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics

Journal of Molecular Biology 2010 397:852-863
Cheng, L. Zhu, Jiang Hui, W. H. Zhang, X. Honig, B. Fang, Q. Zhou, Z. H.

Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement

Journal of Molecular Biology 2010 397:835-851
Zhu, Jiang Cheng, L. Fang, Q. Zhou, Z. H. Honig, B.

Crystal structure of human antibody 2909 reveals conserved features of quaternary structure-specific antibodies that potently neutralize HIV-1

Journal of Virology 2011 85:2524-2535
Changela, A. Wu, X. Yang, Y. Zhang, B. Zhu, Jiang Nardone, G. A. O'Dell, S. Pancera, M. Gorny, M. K. Phogat, S. Robinson, J. E. Stamatatos, L. Zolla-Pazner, S. Mascola, J. R. Kwong, P. D.

Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach

Proceedings of the National Academy of Sciences of the United States of America 2011 108:10133-10138
Zhu, Jiang Yu, Y. Ulbrich, M. H. Li, M. H. Isacoff, E. Y. Honig, B. Yang, J.