Adam Liwo

Publication Activity (10 Years)

Years Active: 1984-2024
Publications (10 Years): 22

Top Topics

Protein Structure

Amino Acid Sequences

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

Publications

Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. J. Chem. Inf. Model. 64 (4) (2024)
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems. Comput. Phys. Commun. 298 (2024)
Adam K. Sieradzan, Jordi Sans-Duñó, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Henryk Leszczynski, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. J. Comput. Chem. 44 (4) (2023)
Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
Long-time scale simulations of virus-like particles from three human-norovirus strains. J. Comput. Chem. 44 (16) (2023)
Emilia A. Lubecka, Adam Liwo
A coarse-grained approach to NMR-data-assisted modeling of protein structures. J. Comput. Chem. 43 (31) (2022)
Emilia A. Lubecka, Adam Liwo
ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons. J. Comput. Chem. 42 (22) (2021)
Pawel Krupa, Agnieszka S. Karczynska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. Bioinform. 37 (11) (2021)
Mateusz Kogut, Zhou Gong, Chun Tang, Adam Liwo
Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures. J. Comput. Chem. 42 (29) (2021)
Agnieszka S. Karczynska, Karolina Zieba, Urszula Uciechowska, Magdalena A. Mozolewska, Pawel Krupa, Emilia A. Lubecka, Agnieszka G. Lipska, Celina Sikorska, Sergey A. Samsonov, Adam K. Sieradzan, Artur Gieldon, Adam Liwo, Rafal Slusarz, Magdalena Slusarz, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. J. Chem. Inf. Model. 60 (3) (2020)
Emilia A. Lubecka, Adam Liwo
Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints. J. Comput. Chem. 40 (25) (2019)
Emilia A. Lubecka, Adam K. Sieradzan, Cezary Czaplewski, Pawel Krupa, Adam Liwo
High Performance Computing with Coarse Grained Model of Biological Macromolecules. Supercomput. Front. Innov. 5 (2) (2018)
Adam K. Sieradzan, Artur Gieldon, Yanping Yin, Yi He, Harold A. Scheraga, Adam Liwo
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. J. Comput. Chem. 39 (28) (2018)
Cezary Czaplewski, Agnieszka S. Karczynska, Adam K. Sieradzan, Adam Liwo
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. 58 (1) (2018)
Agnieszka S. Karczynska, Cezary Czaplewski, Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Adam Liwo
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. J. Comput. Chem. 38 (31) (2017)
Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer
data analytics and indexing of protein trajectories. J. Comput. Chem. 38 (16) (2017)
Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. 57 (9) (2017)
Magdalena A. Mozolewska, Pawel Krupa, Bartlomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. J. Chem. Inf. Model. 56 (11) (2016)
Pawel Krupa, Magdalena A. Mozolewska, Marta Wisniewska, Yanping Yin, Yi He, Adam K. Sieradzan, Robert Ganzynkowicz, Agnieszka G. Lipska, Agnieszka S. Karczynska, Magdalena Slusarz, Rafal Slusarz, Artur Gieldon, Cezary Czaplewski, Dawid Jagiela, Bartlomiej Zaborowski, Harold A. Scheraga, Adam Liwo
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinform. 32 (21) (2016)
Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo
Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field. J. Chem. Inf. Model. 55 (6) (2015)
Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer
It-Situ Data Analysis of Protein Folding Trajectories. CoRR (2015)
Bartlomiej Zaborowski, Dawid Jagiela, Cezary Czaplewski, Anna Halabis, Agnieszka Lewandowska, Wioletta Zmudzinska, Stanislaw Oldziej, Agnieszka S. Karczynska, Christian Omieczynski, Tomasz K. Wirecki, Adam Liwo
A Maximum-Likelihood Approach to Force-Field Calibration. J. Chem. Inf. Model. 55 (9) (2015)
Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga
Coarse-grained model of nucleic acid bases. J. Comput. Chem. 31 (8) (2010)
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. J. Comput. Chem. 31 (6) (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)
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. J. Comput. Chem. 31 (6) (2010)
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. J. Comput. Chem. 30 (13) (2009)
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. J. Comput. Chem. 26 (3) (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. J. Comput. Chem. 23 (1) (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. J. Comput. Chem. 23 (11) (2002)
Rajmund Kazmierkiewicz, Adam Liwo, Harold A. Scheraga
Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. J. Comput. Chem. 23 (7) (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)
Harold A. Scheraga, Jooyoung Lee, Jaroslaw Pillardy, Yuan-Jie Ye, Adam Liwo, Daniel R. Ripoll
Surmounting the Multiple-Minima Problem in Protein Folding. J. Glob. Optim. 15 (3) (1999)
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. J. Comput. Chem. 19 (3) (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. Comput. Chem. 21 (2) (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. J. Comput. Chem. 18 (13) (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. J. Comput. Chem. 18 (7) (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. J. Comput. Chem. 18 (7) (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. J. Comput. Chem. 16 (9) (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. J. Comput. Aided Mol. Des. 7 (6) (1993)
Adam Liwo, Monika Tarnowska, Zbigniew Grzonka, Anna Tempczyk
Modified Free-Wilson Method for the Analysis of Biological Activity Data. Comput. Chem. 16 (1) (1992)
Adam Liwo, Anna Tempczyk, Zbigniew Grzonka
Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues. J. Comput. Aided Mol. Des. 3 (3) (1989)
Adam Liwo, Anna Tempczyk, Zbigniew Grzonka
Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues. J. Comput. Aided Mol. Des. 2 (4) (1989)
Jaroslaw Kostrowicki, Adam Liwo, Krzysztof Sokolowski
A comparative study on some methods for computing equilibrium concentrations. Comput. Chem. 12 (4) (1988)
Jaroslaw Kostrowicki, Adam Liwo
A general method for the determination of the stoichiometry of unknown species in multicomponent systems from physicochemical measurements. Comput. Chem. 11 (3) (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. Comput. Chem. 8 (2) (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. Comput. Chem. 8 (2) (1984)