Computational Biology

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.