A new progressive-iterative algorithm for multiple structure alignment. - Dmitry Lupyan; Alejandra Leo-Macias; Angel R. Ortiz (Bioinform., 2005)

Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. - Dmitry Lupyan; Yuriy A. Abramov; Woody Sherman (J. Comput. Aided Mol. Des., 2012)

Erratum to: Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. - Dmitry Lupyan; Yuriy A. Abramov; Woody Sherman (J. Comput. Aided Mol. Des., 2013)

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics. - Haoyu S. Yu; Cen Gao; Dmitry Lupyan; Yujie Wu; Takayuki Kimura; Chuanjie Wu; Leif D. Jacobson; Edward Harder; Robert Abel; Lingle Wang (J. Chem. Inf. Model., 2019)

Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands. - Ara M. Abramyan; Anna Bochicchio; Chuanjie Wu; Wolfgang Damm; David R. Langley; Devleena Shivakumar; Dmitry Lupyan; Lingle Wang; Edward Harder; Eliud O. Oloo (J. Chem. Inf. Model., 2025)