Graphical handling of wide-ranging data: graphing of photon cross-section data. - Dusanka Janezic; Matej Penca; B. B. Lide; David R. Lide (J. Chem. Inf. Comput. Sci., 1990)

Implicit Runge-Kutta method for molecular dynamics integration. - Dusanka Janezic; Bojan Orel (J. Chem. Inf. Comput. Sci., 1993)

Parallel Algorithm for Molecular Dynamics Integration. - Roman Trobec; Izidor Jerebic; Dusanka Janezic (Parallel Comput., 1993)

Parallelization of an Implicit Runge-Kutta Method for Molecular Dynamics Integration. - Dusanka Janezic; Roman Trobec (J. Chem. Inf. Comput. Sci., 1994)

Harmonic Analysis of Large Systems. I. Methodology. - Bernard R. Brooks; Dusanka Janezic; Martin Karplus (J. Comput. Chem., 1995)

Harmonic Analysis of Large Systems. II. Comaprison of Different Protein Models. - Dusanka Janezic; Martin Karplus (J. Comput. Chem., 1995)

Harmonic Analysis of Large Systems. III. Comparison with Molecular Dynamics. - Dusanka Janezic; Richard M. Venable; Martin Karplus (J. Comput. Chem., 1995)

An Efficient Symplectic Integration Algorithm for Molecular Dynamics Simulations. - Dusanka Janezic; Franci Merzel (J. Chem. Inf. Comput. Sci., 1995)

Comparison of Parallel Verlet and Implicit Runge-Kutta Methods for Molecular Dynamics Integration. - Roman Trobec; Dusanka Janezic (J. Chem. Inf. Comput. Sci., 1995)

Computational Complexity of Split Symplectic MD Integration Method. - Roman Trobec; Franci Merzel; Dusanka Janezic (PARCO, 1997)

Split Integration Symplectic Method for Molecular Dynamics Integration. - Dusanka Janezic; Franci Merzel (J. Chem. Inf. Comput. Sci., 1997)

The Complexity of Parallel Symplectic Molecular Dynamics Algorithms. - Roman Trobec; Franci Merzel; Dusanka Janezic (J. Chem. Inf. Comput. Sci., 1997)

Long Time Step MD Simulations Using Split Integration Symplectic Method. - Dusanka Janezic; Franci Merzel (Computational Molecular Dynamics, 1999)

Molecular Dynamics Integration Time Step Dependence of the Split Integration Symplectic Method on System Density. - Dusanka Janezic; Matej Praprotnik (J. Chem. Inf. Comput. Sci., 2003)

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

Reviews in Computational Chemistry. Volume 19 Edited by Kenny B. Lipkowitz, Raima Larter, and Thomas R. Cundari. Wiley-VCH 2003, ISBN 0-471-23585-7. - Urban Borstnik; Dusanka Janezic (J. Chem. Inf. Model., 2004)

The Eighteenth International Course & Conference on the Interfaces among Mathematics, Chemistry & Computer Sciences June 23-28, 2003 Dubrovnik, Croatia. - Dusanka Janezic; Ante Graovac (J. Chem. Inf. Model., 2004)

Enumeration of Conjugated Circuits in Nanotubes. - István Lukovits; Dusanka Janezic (J. Chem. Inf. Model., 2004)

Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers. - Urban Borstnik; Dusanka Janezic (J. Chem. Inf. Model., 2005)

Periodic Cages. - Mircea V. Diudea; Csaba L. Nagy; Ioan Silaghi-Dumitrescu; Ante Graovac; Dusanka Janezic; Drazen Vikic-Topic (J. Chem. Inf. Model., 2005)

The Regional Biophysics Meeting March 16-20, 2005, Zrece, Slovenia. - Dusanka Janezic (J. Chem. Inf. Model., 2005)

Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations. - Matej Praprotnik; Dusanka Janezic (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)

Retro-Leapfrog and Related Retro Map Operations. - Aniela E. Vizitiu; Mircea V. Diudea; Sonja Nikolic; Dusanka Janezic (J. Chem. Inf. Model., 2006)

A Branch and Bound Algorithm for Matching Protein Structures. - Janez Konc; Dusanka Janezic (ICANNGA (2), 2007)

Cluj and Related Polynomials Applied in Correlating Studies. - Mircea V. Diudea; Aniela E. Vizitiu; Dusanka Janezic (J. Chem. Inf. Model., 2007)

Protein-Protein Binding-Sites Prediction by Protein Surface Structure Conservation. - Janez Konc; Dusanka Janezic (J. Chem. Inf. Model., 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)

Protein Surface Conservation in Binding Sites. - Nejc Carl; Janez Konc; Dusanka Janezic (J. Chem. Inf. Model., 2008)

Topological Complexity of Molecules. - Dusanka Janezic; Ante Milicevic; Sonja Nikolic; Nenad Trinajstic (Encyclopedia of Complexity and Systems Science, 2009)

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. - Janez Konc; Dusanka Janezic (Bioinform., 2010)

Protein-Protein Binding Site Prediction by Local Structural Alignment. - Nejc Carl; Janez Konc; Blaz Vehar; Dusanka Janezic (J. Chem. Inf. Model., 2010)

ProBiS: a web server for detection of structurally similar protein binding sites. - Janez Konc; Dusanka Janezic (Nucleic Acids Res., 2010)

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations. - Urban Borstnik; Benjamin T. Miller; Bernard R. Brooks; Dusanka Janezic (J. Comput. Chem., 2011)

Parallel-ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites. - Janez Konc; Matjaz Depolli; Roman Trobec; Kati Rozman; Dusanka Janezic (J. Comput. Chem., 2012)

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)

ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures. - Janez Konc; Tomo Cesnik; Joanna Trykowska Konc; Matej Penca; Dusanka Janezic (J. Chem. Inf. Model., 2012)

ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins. - Janez Konc; Dusanka Janezic (Nucleic Acids Res., 2012)

Exact Parallel Maximum Clique Algorithm for General and Protein Graphs. - Matjaz Depolli; Janez Konc; Kati Rozman; Roman Trobec; Dusanka Janezic (J. Chem. Inf. Model., 2013)

Structurally Conserved Binding Sites of Hemagglutinin as Targets for Influenza Drug and Vaccine Development. - Muhammad Yusuf; Janez Konc; Sy Bing Choi; Joanna Trykowska Konc; Nurul Bahiyah Ahmad Khairudin; Dusanka Janezic; Habibah A. Wahab (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)

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites. - Janez Konc; Dusanka Janezic (Nucleic Acids Res., 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 enzyme-ligand binding in drug discovery. - Janez Konc; Samo Lesnik; Dusanka Janezic (J. Cheminformatics, 2015)

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. - Janez Konc; Benjamin T. Miller; Tanja Stular; Samo Lesnik; H. Lee Woodcock III; Bernard R. Brooks; Dusanka Janezic (J. Chem. Inf. Model., 2015)

LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors. - Samo Lesnik; Tanja Stular; Boris Brus; Damijan Knez; Stanislav Gobec; Dusanka Janezic; Janez Konc (J. Chem. Inf. Model., 2015)

Ligand-based virtual screening interface between PyMOL and LiSiCA. - Athira Dilip; Samo Lesnik; Tanja Stular; Dusanka Janezic; Janez Konc (J. Cheminformatics, 2016)

H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. - Muhammad Yusuf; Nornisah Mohamed; Suriyati Mohamad; Dusanka Janezic; K. V. Damodaran; Habibah A. Wahab (J. Chem. Inf. Model., 2016)

BoBER: web interface to the base of bioisosterically exchangeable replacements. - Samo Lesnik; Blaz Skrlj; Nika Erzen; Urban Bren; Stanislav Gobec; Janez Konc; Dusanka Janezic (J. Cheminformatics, 2017)

GenProBiS: web server for mapping of sequence variants to protein binding sites. - Janez Konc; Blaz Skrlj; Nika Erzen; Tanja Kunej; Dusanka Janezic (Nucleic Acids Res., 2017)

Identification of Conserved Water Sites in Protein Structures for Drug Design. - Marko Jukic; Janez Konc; Stanislav Gobec; Dusanka Janezic (J. Chem. Inf. Model., 2017)

Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. - Katarina Kores; Samo Lesnik; Urban Bren; Dusanka Janezic; Janez Konc (J. Chem. Inf. Model., 2019)

ProBiS-Dock Database: A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design. - Janez Konc; Samo Lesnik; Blaz Skrlj; Dusanka Janezic (J. Chem. Inf. Model., 2021)

ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites. - Janez Konc; Dusanka Janezic (J. Chem. Inf. Model., 2022)

ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison. - Janez Konc; Samo Lesnik; Blaz Skrlj; Matej Sova; Matic Proj; Damijan Knez; Stanislav Gobec; Dusanka Janezic (J. Chem. Inf. Model., 2022)

Advanced clique algorithms for protein product graphs. - Janez Konc; Dusanka Janezic (Art Discret. Appl. Math., 2025)