Global Energy Minimization of Small Molecules Combining Constraint Logic Programming and Molecular Mechanics. - Darko Zupanic; Milan Hodoscek; Nada Lavrac; Igor Mozetic (J. Chem. Inf. Comput. Sci., 1997)

Computational Chemistry on Commodity-Type Computers. - Marc C. Nicklaus; Robert W. Williams; Bruno Bienfait; Eric S. Billings; Milan Hodoscek (J. Chem. Inf. Comput. Sci., 1998)

Prediction of Enzyme Binding: Human Thrombin Inhibition Study by Quantum Chemical and Artificial Intelligence Methods Based on X-ray Structures. - Gregor Mlinsek; Marjana Novic; Milan Hodoscek; Tomaz Solmajer (J. Chem. Inf. Comput. Sci., 2001)

Transition State Structure and Energetics of the N2O + X (X = Cl, Br) Reactions. - Antonija Lesar; Milan Hodoscek (J. Chem. Inf. Comput. Sci., 2002)

Enthalpy of the Gas-Phase CO2 + Mg Reaction from ab Initio Total Energies. - Antonija Lesar; Saa Prebil; Milan Hodoscek (J. Chem. Inf. Comput. Sci., 2002)

Improving the Performance of Molecular Dynamics Simulations on Parallel Clusters. - Urban Borstnik; Milan Hodoscek; Dusanka Janezic (J. Chem. Inf. Model., 2004)

Development and Validation of Empirical Force Field Parameters for Netropsin. - Urban Bren; Milan Hodoscek; Joze Koller (J. Chem. Inf. Model., 2005)

Quantum Mechanical Study of the Potential Energy Surface of the ClO + NO2 Reaction. - Sasa Kovacic; Antonija Lesar; Milan Hodoscek (J. Chem. Inf. Model., 2005)

New force field for calcium binding sites in annexin-membrane complexes. - Franci Merzel; Milan Hodoscek; Dusanka Janezic; Alain Sanson (J. Comput. Chem., 2006)

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. - H. Lee Woodcock III; Milan Hodoscek; Andrew T. B. Gilbert; Peter M. W. Gill; Henry F. Schaefer III; Bernard R. Brooks (J. Comput. Chem., 2007)

New all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve. - Matej Praprotnik; Stanko Hocevar; Milan Hodoscek; Matej Penca; Dusanka Janezic (J. Comput. Chem., 2008)

CHARMMing: A New, Flexible Web Portal for CHARMM. - Benjamin T. Miller; Rishi P. Singh; Jeffery B. Klauda; Milan Hodoscek; Bernard R. Brooks; H. Lee Woodcock III (J. Chem. Inf. Model., 2008)

Copper(II) Ion Binding to Cellular Prion Protein. - Jernej Zidar; Elizabeta T. Pirc; Milan Hodoscek; Peter Bukovec (J. Chem. Inf. Model., 2008)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues. - Nejc Carl; Milan Hodoscek; Blaz Vehar; Janez Konc; Bernard R. Brooks; Dusanka Janezic (J. Chem. Inf. Model., 2012)

Ligand Binding Site Identification by Higher Dimension Molecular Dynamics. - Achani K. Yatawara; Milan Hodoscek; Dale F. Mierke (J. Chem. Inf. Model., 2013)

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison. - Janez Konc; Milan Hodoscek; Mitja Ogrizek; Joanna Trykowska Konc; Dusanka Janezic (PLoS Comput. Biol., 2013)

Structural Insight into the Unique Binding Properties of Pyridylethanol(phenylethyl)amine Inhibitor in Human CYP51. - Urska Zelenko; Milan Hodoscek; Damjana Rozman; Simona Golic Grdadolnik (J. Chem. Inf. Model., 2014)

Molecular dynamics to enhance structure-based virtual screening on cathepsin B. - Mitja Ogrizek; Samo Turk; Samo Lesnik; Izidor Sosic; Milan Hodoscek; Bojana Mirkovic; Janko Kos; Dusanka Janezic; Stanislav Gobec; Janez Konc (J. Comput. Aided Mol. Des., 2015)

Modeling a learning organization using a molecular network framework. - Matej Janezic; Vlado Dimovski; Milan Hodoscek (Comput. Educ., 2018)

Potential Energy Function for Fentanyl-Based Opioid Pain Killers. - Samo Lesnik; Milan Hodoscek; Urban Bren; Christoph Stein; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2020)

Loop Grafting between Similar Local Environments for Fc-Silent Antibodies. - Samo Lesnik; Milan Hodoscek; Barbara Podobnik; Janez Konc (J. Chem. Inf. Model., 2020)

CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs. - Thomas Giannos; Samo Lesnik; Urban Bren; Milan Hodoscek; Tatiana Domratcheva; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2021)