Maciej Długosz, Joanna Trylska,  Describing Properties on Protein Surfaces with Surface Diver, submitted

Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska, RedMD - reduced molecular dynamics package, J. Comput. Chem., accepted

Maciej Dlugosz, Joanna Trylska, Aminoglycoside Association Pathways with the 30S Ribosomal Subunit, submitted

Piotr Setny, Joanna Trylska; Search for Novel Aminoglycoside Derivatives by Combining Fragment-based Virtual Screening and 3D-QSAR Scoring, J. Chem. Inf. Model., accepted

Julia Romanowska, Piotr Setny, Joanna Trylska; Molecular dynamics study of the ribosomal A-site, J. Phys. Chem. B., 112:15227-15243, 2008

Maciej Dlugosz, Joanna Trylska; Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition, J. Chem. Phys., 129:015103, 2008

Maciej Dlugosz, Jan M. Antosiewicz, Joanna Trylska; Association of Aminoglycosidic Antibiotics with the Ribosomal A-site Studied with Brownian Dynamics, J. Chem. Theory Comput., 4:549-559, 2008 Cover figure

Magdalena Gruziel, Pawel Grochowski, Joanna Trylska; The Poisson-Boltzmann model for tRNA. Assessment of the calculation set-up and ionic concentration cutoff, J. Comp. Chem., 29:1970-1981, 2008

Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Joerg Langowski, Jeremy Smith; Coarse-grained Force Field for the Nucleosome from Self-consistent Multiscaling, J. Comp. Chem., 29:1429-1439, 2008

Pawel Grochowski, Joanna Trylska; Continuum Molecular Electrostatics, Salt Effects and Counterion Binding. A Review of the Poisson-Boltzmann Model and its Modifications, Biopolymers, 89:93-113, 2008

Joanna Trylska, Valentina Tozzini, Chia-en Chang, J. Andrew McCammon; HIV-1 Protease Substrate Binding and Product Release Pathways Explored with Coarse-Grained Molecular Dynamics, Biophys. J., 92:4179-4187, 2007

Chia-en Chang, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations, Chem. Biol. & Drug Design, 69:5-13, 2007 Cover figure

Valentina Tozzini, Joanna Trylska, Chia-en Chang, J. Andrew McCammon; Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-Grained Model, J. Struct. Biol., 157:606-615, 2007

Grace Yang, Joanna Trylska, Yitzhak Tor, J. Andrew McCammon; Binding of Aminoglycosidic Antibiotics to the Oligonucleotide A-site Model and 30S Ribosomal Subunit: Poisson-Boltzmann Model, Thermal Denaturation and Fluorescence Studies, J. Med. Chem., 49:5478-5490, 2006

Adam Gorecki, Joanna Trylska, Bogdan Lesyng; Causality Relations in Molecular Dynamics Investigated with Multi-Variable Autoregressive Model, Europhys. Lett., 75:503-509, 2006

Chia-en Chang, Tongye Shen, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model, Biophys. J., 90:3880-3885, 2006

David D. L. Minh, Chia-en Chang, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics J. Am. Chem. Soc., 128:6006-6007, 2006

Kay Hamacher, Joanna Trylska, J. Andrew McCammon; Dependency Map of Proteins in the Small Ribosomal Subunit, PLoS Comp. Biol., 2:0080-0087, 2006

Robert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks, III, J. Andrew McCammon; Electrostatic Properties of Cowpea Chlorotic Mottle Virus and Cucumber Mosaic Virus Capsids, Biopolymers, 82:106-120, 2006

Joanna Trylska, J. Andrew McCammon, Charles L. Brooks III; Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent Approach, J. Am. Chem. Soc., 127:11125-11133, 2005

Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Exploring Global Motions and Correlations in the Ribosome, Biophys. J., 89:1455-1463, 2005

Joanna Trylska, Robert Konecny, Florence Tama, Charles L. Brooks III, J. Andrew McCammon; Ribosome motions modulate electrostatic properties, Biopolymers, 74:423-431, 2004 Cover figure 

Joanna Trylska, Pawel Grochowski, J. Andrew McCammon; The Role of Hydrogen Bonding in the Enzymatic Reaction Catalyzed by HIV-1 Protease Protein Science, 13:513-528, 2004

Joanna Trylska, Piotr Bala, Maciej Geller, Pawel Grochowski; Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease Biophys. J., 83:794-807, 2002

Joanna Trylska, Pawel Grochowski, Maciej Geller; Parameterization of the Approximate Valence Bond (AVB) Method to Describe Potential Energy Surface in the Reaction Catalyzed by HIV-1 Protease Int. J. Quant. Chem., 82:86-103, 2001

Roman Bogacewicz, Joanna Trylska, Maciej Geller; Ligand design package (LUDI - MSI) applied to known inhibitors of the HIV-1 protease. Test of performance Acta Poloniae Pharmaceutica, 57:25-28, 2000

Joanna Trylska, Jan Antosiewicz, Maciej Geller, C. N. Hodge, Ronald Klabe, Martha S. Head, Michael K. Gilson; Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease Protein Science, 8:180-195, 1999

Books and Proceedings

Marcin Szypowski, Adam Gorecki, Joanna Trylska, RedMD - a New Package for Reduced Molecular Dynamics, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:389-392, ISBN 978-3-9810843-6-8, 2008

Katarzyna Kulczycka, Maciej Dlugosz, Joanna Trylska, Internal Dynamics of Elongation Factors G and Tu Studied with All-atom and Coarse-grained Molecular Dynamics, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:277-280, ISBN 978-3-9810843-6-8, 2008

Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jeremy Smith, Joerg Langowski, Global Motions in the Nucleosome Explored using a Coarse-grain Model, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:141-144, ISBN 978-3-9810843-6-8, 2008

Maciej Dlugosz, Joanna Trylska, Association of Neamine and its Derivative with the Ribosomal A-site RNA, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:81-84, ISBN 978-3-9810843-6-8, 2008

Adam Gorecki, Joanna Trylska, Bogdan Lesyng; Causality and Correlation Analyses of Molecular Dynamics Simulation Data, In: From Computational Biophysics to Systems Biology (CBSB07), John von Neumann Institute for Computing Symposium May 2-4 2007, 36:25-30, ISBN: 978-3-9810843-2-0, 2007

Magda Gruziel, Piotr Kmiec, Joanna Trylska, Bogdan Lesyng; Selected Microscopic and Mezoscopic Modelling Tools and Models - an Overview, In: Molecular Materials with Specific Interactions: Modeling and Design, Ed. A. W. Sokalski, Series Title: Challenges and Advances in Chemistry and Physics, Springer, Dordrecht, The Netherlands, 4:203-224, ISBN-10 1-4020-5371-1 (HB), 2007 

Joanna Trylska, Piotr Bala, Maciej Geller, Pawel Grochowski;  Quantum-Classical Molecular Dynamics Simulations in the Studies of the Reaction Catalyzed by HIV-1 Protease In: Simulation in Research and Development, Polish Association for Computer Simulation, p. 269-276, ISBN:83-7365-048-2, 2003 

Piotr Bala, Maciej Geller, Krzysztof Ginalski, Pawel Grochowski, Joanna Trylska, Bogdan Lesyng; Approximate Valence Bond Method - A Fast Generator of Quantum Potentials for Molecular Simulations In: Modelling and Simulation: A Tool for the Next Millenium, 13th European Simulation Multiconference, June 1-4, 1999, Warsaw, Poland, p. 181-183, Society for Computer Simulation International, 1999

Maciej Geller, Joanna Trylska, Jan Antosiewicz; HIV-1 Protease and its Inhibitors In: Theoretical and Computational Methods in Genome Research, Sandor Suhai Plenum Press, p. 237-242, ISBN:030645503X, 1997