Adam Liwo - researchr alias

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Viewing Publication 1 - 45 from 45

2024

Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein StructuresMateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo. jcisd, 64(4):1377-1393, February 2024. [doi]

2023

2022

A coarse-grained approach to NMR-data-assisted modeling of protein structuresEmilia A. Lubecka, Adam Liwo. jcc, 43(31):2047-2059, 2022. [doi]

2021

2020

2019

Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraintsEmilia A. Lubecka, Adam Liwo. jcc, 40(25):2164-2178, 2019. [doi]

2018

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamicsCezary Czaplewski, Agnieszka Karczynska, Adam K. Sieradzan, Adam Liwo. nar, 46(Webserver-Issue), 2018. [doi]

Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and DynamicsPawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo. jcisd, 58(1):206, 2018. [doi]

High Performance Computing with Coarse Grained Model of Biological MacromoleculesEmilia A. Lubecka, Adam K. Sieradzan, Cezary Czaplewski, Pawel Krupa, Adam Liwo. superfri, 5(2):63-75, 2018. [doi]

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fieldsAdam K. Sieradzan, Artur Gieldon, Yanping Yin, Yi He, Harold A. Scheraga, Adam Liwo. jcc, 39(28):2360-2370, 2018. [doi]

2017

2016

2015

2010

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 meUrszula Kozlowska, Adam Liwo, Harold A. Scheraga. jcc, 31(6):1143-1153, 2010. [doi]

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. ResulUrszula Kozlowska, Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga. jcc, 31(6):1154-1167, 2010. [doi]

Coarse-grained model of nucleic acid basesMaciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga. jcc, 31(8):1644-1655, 2010. [doi]

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding SimulationsStanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga. bibe 2010: 263-266 [doi]

2009

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

2005

Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean forceJoanna Makowska, Mariusz Makowski, Adam Liwo, Lech Chmurzynski. jcc, 26(3):235-242, 2005. [doi]

2002

2000

UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody termsAdam 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. recomb 2000: 193-200 [doi]

1999

Surmounting the Multiple-Minima Problem in Protein FoldingHarold A. Scheraga, Jooyoung Lee, Jaroslaw Pillardy, Yuan-Jie Ye, Adam Liwo, Daniel R. Ripoll. jgo, 15(3):235-260, 1999. [doi]

1998

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

1997

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 dataAdam Liwo, Stanislaw Oldziej, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Harold A. Scheraga. jcc, 18(7):849-873, 1997. [doi]

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

A New Approach to the Resolution of the Excitation-emission Spectra of Multicomponent SystemsAdam Liwo, Piotr Skurski, Stanislaw Oldziej, Leszek Lankiewicz, Joanna Malicka, Wieslaw Wiczk. CANDC, 21(2):89-95, 1997. [doi]

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 optimizationAdam Liwo, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Stanislaw Oldziej, Harold A. Scheraga. jcc, 18(7):874-887, 1997. [doi]

1995

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

1993

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

1992

Modified Free-Wilson Method for the Analysis of Biological Activity DataAdam Liwo, Monika Tarnowska, Zbigniew Grzonka, Anna Tempczyk. CANDC, 16(1):1-9, 1992. [doi]

1989

Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analoguesAdam Liwo, Anna Tempczyk, Zbigniew Grzonka. jcamd, 2(4):281-309, 1989. [doi]

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 analoguesAdam Liwo, Anna Tempczyk, Zbigniew Grzonka. jcamd, 3(3):261-284, 1989. [doi]

1988

A comparative study on some methods for computing equilibrium concentrationsJaroslaw Kostrowicki, Adam Liwo, Krzysztof Sokolowski. CANDC, 12(4):293-299, 1988. [doi]

1987

A general method for the determination of the stoichiometry of unknown species in multicomponent systems from physicochemical measurementsJaroslaw Kostrowicki, Adam Liwo. CANDC, 11(3):195-210, 1987. [doi]

1984

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 concentrationsJaroslaw Kostrowicki, Adam Liwo. CANDC, 8(2):91-99, 1984. [doi]

DECFAM - A new computer oriented algorithm for the determination of equilibrium constants from potentiometric and/or spectrophotometric measurements - II: Methods based on analytical expressionsJaroslaw Kostrowicki, Adam Liwo. CANDC, 8(2):101-105, 1984. [doi]

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