Adam Liwo

48 papers B 1C 1Journal 45
YearRankTypeTitle / Venue / Authors
2024 J jnl
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.
J. Chem. Inf. Model.
Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo
2024 J jnl
Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems.
Comput. Phys. Commun.
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
2023 J jnl
Long-time scale simulations of virus-like particles from three human-norovirus strains.
J. Comput. Chem.
Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
2023 J jnl
Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins.
J. Comput. Chem.
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
2023 J jnl
UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.
Bioinform.
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
2022 J jnl
A coarse-grained approach to NMR-data-assisted modeling of protein structures.
J. Comput. Chem.
Emilia A. Lubecka, Adam Liwo
2021 J jnl
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.
Emilia A. Lubecka, Adam Liwo
2021 J jnl
Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures.
J. Comput. Chem.
Mateusz Kogut, Zhou Gong, Chun Tang, Adam Liwo
2021 J jnl
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.
Bioinform.
Pawel Krupa, Agnieszka S. Karczynska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski
2020 J jnl
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.
J. Chem. Inf. Model.
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
2019 J jnl
Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints.
J. Comput. Chem.
Emilia A. Lubecka, Adam Liwo
2018 J jnl
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.
J. Comput. Chem.
Adam K. Sieradzan, Artur Gieldon, Yanping Yin, Yi He, Harold A. Scheraga, Adam Liwo
2018 J jnl
Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.
J. Chem. Inf. Model.
Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
2018 J jnl
High Performance Computing with Coarse Grained Model of Biological Macromolecules.
Supercomput. Front. Innov.
Emilia A. Lubecka, Adam K. Sieradzan, Cezary Czaplewski, Pawel Krupa, Adam Liwo
2018 J jnl
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
Nucleic Acids Res.
Cezary Czaplewski, Agnieszka S. Karczynska, Adam K. Sieradzan, Adam Liwo
2017 J jnl
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.
J. Comput. Chem.
Agnieszka S. Karczynska, Cezary Czaplewski, Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Adam Liwo
2017 J jnl
Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.
J. Chem. Inf. Model.
Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
2016 J jnl
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Bioinform.
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
2016 J jnl
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.
Magdalena A. Mozolewska, Pawel Krupa, Bartlomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
2015 J jnl
A Maximum-Likelihood Approach to Force-Field Calibration.
J. Chem. Inf. Model.
Bartlomiej Zaborowski, Dawid Jagiela, Cezary Czaplewski, Anna Halabis, Agnieszka Lewandowska, Wioletta Zmudzinska, Stanislaw Oldziej, Agnieszka S. Karczynska, Christian Omieczynski, Tomasz K. Wirecki, Adam Liwo
2015 J jnl
It-Situ Data Analysis of Protein Folding Trajectories.
CoRR
Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer
2015 J jnl
Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.
J. Chem. Inf. Model.
Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo
2010 J jnl
Coarse-grained model of nucleic acid bases.
J. Comput. Chem.
Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga
2010 J jnl
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.
Urszula Kozlowska, Adam Liwo, Harold A. Scheraga
2010 J jnl
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.
Urszula Kozlowska, Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga
2010 C conf
Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations.
BIBE
Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga
2009 J jnl
Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field.
J. Comput. Chem.
Yi He, Yi Xiao, Adam Liwo, Harold A. Scheraga
2009 — ch.
Global Optimization in Protein Folding.
Encyclopedia of Optimization
Daniel R. Ripoll, Adam Liwo, Harold A. Scheraga
2005 J jnl
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.
Joanna Makowska, Mariusz Makowski, Adam Liwo, Lech Chmurzynski
2002 J jnl
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.
Maciej Bobrowski, Adam Liwo, Stanislaw Oldziej, Danuta Jeziorek, Tadeusz Ossowski
2002 J jnl
Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method.
J. Comput. Chem.
Rajmund Kazmierkiewicz, Adam Liwo, Harold A. Scheraga
2002 J jnl
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.
J. Comput. Chem.
Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova
2000 B conf
UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms.
RECOMB
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
1999 J jnl
Surmounting the Multiple-Minima Problem in Protein Folding.
J. Glob. Optim.
Harold A. Scheraga, Jooyoung Lee, Jaroslaw Pillardy, Yuan-Jie Ye, Adam Liwo, Daniel R. Ripoll
1998 J jnl
United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
J. Comput. Chem.
Adam Liwo, Rajmund Kazmierkiewicz, Cezary Czaplewski, Malgorzata Groth, Stanislaw Oldziej, Ryszard J. Wawak, Shelly Rackovsky, Matthew R. Pincus, Harold A. Scheraga
1997 J jnl
A New Approach to the Resolution of the Excitation-emission Spectra of Multicomponent Systems.
Comput. Chem.
Adam Liwo, Piotr Skurski, Stanislaw Oldziej, Leszek Lankiewicz, Joanna Malicka, Wieslaw Wiczk
1997 J jnl
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.
Adam Liwo, Stanislaw Oldziej, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Harold A. Scheraga
1997 J jnl
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.
Adam Liwo, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Stanislaw Oldziej, Harold A. Scheraga
1997 J jnl
MCSCF study of singlet oxygen addition to ethenol - a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups.
J. Comput. Chem.
Adam Liwo, Dariusz Dyl, Danuta Jeziorek, Magorzata Nowacka, Tadeusz Ossowski, Wiesaw Wonicki
1995 J jnl
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.
Daniel R. Ripoll, Marcia S. Pottle, Kenneth D. Gibson, Harold A. Scheraga, Adam Liwo
1993 J jnl
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.
Monika Tarnowska, Adam Liwo, Mark D. Shenderovich, Inta Liepina, Alexander Golbraikh, Zbigniew Grzonka, Anna Tempczyk
1992 J jnl
Modified Free-Wilson Method for the Analysis of Biological Activity Data.
Comput. Chem.
Adam Liwo, Monika Tarnowska, Zbigniew Grzonka, Anna Tempczyk
1989 J jnl
Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues.
J. Comput. Aided Mol. Des.
Adam Liwo, Anna Tempczyk, Zbigniew Grzonka
1989 J jnl
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.
Adam Liwo, Anna Tempczyk, Zbigniew Grzonka
1988 J jnl
A comparative study on some methods for computing equilibrium concentrations.
Comput. Chem.
Jaroslaw Kostrowicki, Adam Liwo, Krzysztof Sokolowski
1987 J jnl
A general method for the determination of the stoichiometry of unknown species in multicomponent systems from physicochemical measurements.
Comput. Chem.
Jaroslaw Kostrowicki, Adam Liwo
1984 J jnl
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.
Jaroslaw Kostrowicki, Adam Liwo
1984 J jnl
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.
Jaroslaw Kostrowicki, Adam Liwo