Adam Liwo
Orcid: 0000-0001-6942-2226
According to our database1,
Adam Liwo
authored at least 48 papers
between 1984 and 2024.
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Bibliography
2024
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.
J. Chem. Inf. Model., February, 2024
Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems.
Comput. Phys. Commun., 2024
2023
Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins.
J. Comput. Chem., February, 2023
Long-time scale simulations of virus-like particles from three human-norovirus strains.
J. Comput. Chem., 2023
2022
J. Comput. Chem., 2022
2021
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., 2021
Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures.
J. Comput. Chem., 2021
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.
Bioinform., 2021
2020
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.
J. Chem. Inf. Model., 2020
2019
Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints.
J. Comput. Chem., 2019
2018
Supercomput. Front. Innov., 2018
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
Nucleic Acids Res., 2018
Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.
J. Chem. Inf. Model., 2018
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.
J. Comput. Chem., 2018
2017
Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.
J. Chem. Inf. Model., September, 2017
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.
J. Comput. Chem., 2017
J. Comput. Chem., 2017
2016
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., 2016
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Bioinform., 2016
2015
Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.
J. Chem. Inf. Model., 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. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.
J. Comput. Chem., 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 method.
J. Comput. Chem., 2010
Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations.
Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010
2009
Proceedings of the Encyclopedia of Optimization, Second Edition, 2009
Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field.
J. Comput. Chem., 2009
2005
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., 2005
2002
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.
J. Comput. Chem., 2002
Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method.
J. Comput. Chem., 2002
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., 2002
2000
UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000
1999
1998
United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
J. Comput. Chem., 1998
1997
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., 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 data.
J. Comput. Chem., 1997
MCSCF study of singlet oxygen addition to ethenol - a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups.
J. Comput. Chem., 1997
A New Approach to the Resolution of the Excitation-emission Spectra of Multicomponent Systems.
Comput. Chem., 1997
1995
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., 1995
1993
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., 1993
1992
Comput. Chem., 1992
1989
Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues.
J. Comput. Aided Mol. Des., 1989
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., 1989
1988
Comput. Chem., 1988
1987
A general method for the determination of the stoichiometry of unknown species in multicomponent systems from physicochemical measurements.
Comput. Chem., 1987
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 concentrations.
Comput. Chem., 1984
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., 1984