Adam Liwo

Urszula Kozlowska, Adam Liwo, Harold A. Scheraga: Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method. Journal of Computational Chemistry 31(6): 1143-1153 (2010)

Urszula Kozlowska, Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga: Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. Journal of Computational Chemistry 31(6): 1154-1167 (2010)

Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga: Coarse-grained model of nucleic acid bases. Journal of Computational Chemistry 31(8): 1644-1655 (2010)

Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga: Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. BIBE 2010: 263-266

Yi He, Yi Xiao, Adam Liwo, Harold A. Scheraga: Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field. Journal of Computational Chemistry 30(13): 2127-2135 (2009)

Daniel R. Ripoll, Adam Liwo, Harold A. Scheraga: Global Optimization in Protein Folding. Encyclopedia of Optimization 2009: 1392-1411

Joanna Makowska, Mariusz Makowski, Adam Liwo, Lech Chmurzynski: Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force. Journal of Computational Chemistry 26(3): 235-242 (2005)

Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova: Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. Journal of Computational Chemistry 23(1): 28-34 (2002)

Rajmund Kazmierkiewicz, Adam Liwo, Harold A. Scheraga: Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. Journal of Computational Chemistry 23(7): 715-723 (2002)

Maciej Bobrowski, Adam Liwo, Stanislaw Oldziej, Danuta Jeziorek, Tadeusz Ossowski: Ab initio study of the mechanism of singlet-dioxygen addition to hydroxyaromatic compounds: Negative evidence for the involvement of peroxa and endoperoxide intermediates. Journal of Computational Chemistry 23(11): 1076-1089 (2002)

Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kazmierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga: UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. RECOMB 2000: 193-200

Adam Liwo, Rajmund Kazmierkiewicz, Cezary Czaplewski, Malgorzata Groth, Stanislaw Oldziej, Ryszard J. Wawak, Shelly Rackovsky, Matthew R. Pincus, Harold A. Scheraga: United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. Journal of Computational Chemistry 19(3): 259-276 (1998)

Adam Liwo, Piotr Skurski, Stanislaw Oldziej, Leszek Lankiewicz, Joanna Malicka, Wieslaw Wiczk: A New Approach to the Resolution of the Excitation-emission Spectra of Multicomponent Systems. Computers & Chemistry 21(2): 89-95 (1997)

Adam Liwo, Stanislaw Oldziej, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Harold A. Scheraga: A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. Journal of Computational Chemistry 18(7): 849-873 (1997)

Adam Liwo, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Stanislaw Oldziej, Harold A. Scheraga: A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization. Journal of Computational Chemistry 18(7): 874-887 (1997)

Adam Liwo, Dariusz Dyl, Danuta Jeziorek, Magorzata Nowacka, Tadeusz Ossowski, Wiesaw Wonicki: MCSCF study of singlet oxygen addition to ethenol - a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups. Journal of Computational Chemistry 18(13): 1668-1681 (1997)

Daniel R. Ripoll, Marcia S. Pottle, Kenneth D. Gibson, Harold A. Scheraga, Adam Liwo: Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer. Journal of Computational Chemistry 16(9): 1153-1163 (1995)

Monika Tarnowska, Adam Liwo, Mark D. Shenderovich, Inta Liepina, Alexander Golbraikh, Zbigniew Grzonka, Anna Tempczyk: A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring. Journal of Computer-Aided Molecular Design 7(6): 699-720 (1993)

Adam Liwo, Monika Tarnowska, Zbigniew Grzonka, Anna Tempczyk: Modified Free-Wilson Method for the Analysis of Biological Activity Data. Computers & Chemistry 16(1): 1-9 (1992)

Jaroslaw Kostrowicki, Adam Liwo, Krzysztof Sokolowski: A comparative study on some methods for computing equilibrium concentrations. Computers & Chemistry 12(4): 293-299 (1988)

Jaroslaw Kostrowicki, Adam Liwo: A general method for the determination of the stoichiometry of unknown species in multicomponent systems from physicochemical measurements. Computers & Chemistry 11(3): 195-210 (1987)

Jaroslaw Kostrowicki, Adam Liwo: DECFAM - A new computer oriented algorithm for the determination of equilibrium constants from potentionmetric and/or spectrophotometric measurements - I: Basic principles of the method and calculations of equilibrium concentrations. Computers & Chemistry 8(2): 91-99 (1984)

Jaroslaw Kostrowicki, Adam Liwo: DECFAM - A new computer oriented algorithm for the determination of equilibrium constants from potentiometric and/or spectrophotometric measurements - II: Methods based on analytical expressions. Computers & Chemistry 8(2): 101-105 (1984)