Multiple-site ligand binding to flexible macromolecules: Separation of global and local conformational change and an iterative mobile clustering approach. - Velin Z. Spassov; Donald Bashford (J. Comput. Chem., 1999)

A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. - W. Jim Zheng; Velin Z. Spassov; Lisa Yan; Paul K. Flook; Sándor Szalma (Comput. Biol. Chem., 2004)

Fully Automated Molecular Mechanics Based Induced Fit Protein-Ligand Docking Method. - Jurgen Koska; Velin Z. Spassov; Allister J. Maynard; Lisa Yan; Nic Austin; Paul K. Flook; C. M. Venkatachalam (J. Chem. Inf. Model., 2008)

A pH-dependent computational approach to the effect of mutations on protein stability. - Velin Z. Spassov; Lisa Yan (J. Comput. Chem., 2016)