Compare Conformer: a program for the rapid comparison of molecular conformers based on interatomic distances and torsion angles. - István Kolossváry; Wayne C. Guida (J. Chem. Inf. Comput. Sci., 1992)

Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space. - István Kolossváry; Wayne C. Guida (J. Comput. Chem., 1993)

Theoretical study of intramolecular hydrogen bonding and molecular geometry of 2-trifluoromethylphenol. - Attila Kovács; István Kolossváry; Gábor I. Csonka; István Hargittai (J. Comput. Chem., 1996)

Simple tests for density functional methods. - Gábor I. Csonka; Nam Anh Nguyen; István Kolossváry (J. Comput. Chem., 1997)

On the Sign of Local Temperature in Molecules. - István Kolossváry (Entropy, 1999)

Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP. - István Kolossváry; Wayne C. Guida (J. Comput. Chem., 1999)

Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3. - István Kolossváry; György M. Keserü (J. Comput. Chem., 2001)

Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy. - Olgun Guvench; Jörg Weiser; Peter S. Shenkin; István Kolossváry; W. Clark Still (J. Comput. Chem., 2002)

Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters. - Kevin J. Bowers; Edmond Chow; Huafeng Xu; Ron O. Dror; Michael P. Eastwood; Brent A. Gregersen; John L. Klepeis; István Kolossváry; Mark A. Moraes; Federico D. Sacerdoti; John K. Salmon; Yibing Shan; et al. (SC, 2006)

Anton, a special-purpose machine for molecular dynamics simulation. - David E. Shaw; Martin M. Deneroff; Ron O. Dror; Jeffrey Kuskin; Richard H. Larson; John K. Salmon; Cliff Young; Brannon Batson; Kevin J. Bowers; Jack C. Chao; Michael P. Eastwood; Joseph Gagliardo; et al. (Commun. ACM, 2008)