Adam Liwo

According to our database1, Adam Liwo authored at least 36 papers between 1984 and 2019.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2019
Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints.
Journal of Computational Chemistry, 2019

2018
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
Nucleic Acids Research, 2018

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.
Journal of Computational Chemistry, 2018

2017
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.
Journal of Computational Chemistry, 2017

In situ data analytics and indexing of protein trajectories.
Journal of Computational Chemistry, 2017

2016
Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field.
Journal of Chemical Information and Modeling, 2016

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Bioinformatics, 2016

2015
A Maximum-Likelihood Approach to Force-Field Calibration.
Journal of Chemical Information and Modeling, 2015

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.
Journal of Chemical Information and Modeling, 2015

It-Situ Data Analysis of Protein Folding Trajectories.
CoRR, 2015

2010
Coarse-grained model of nucleic acid bases.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 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
Global Optimization in Protein Folding.
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.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 2005

2002
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.
Journal of Computational Chemistry, 2002

Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method.
Journal of Computational Chemistry, 2002

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, 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
Surmounting the Multiple-Minima Problem in Protein Folding.
J. Global Optimization, 1999

1998
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, 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.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 1997

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, 1997

A New Approach to the Resolution of the Excitation-emission Spectra of Multicomponent Systems.
Computers & Chemistry, 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.
Journal of Computational Chemistry, 1995

1993
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, 1993

1992
Modified Free-Wilson Method for the Analysis of Biological Activity Data.
Computers & Chemistry, 1992

1989
Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues.
Journal of Computer-Aided Molecular Design, 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.
Journal of Computer-Aided Molecular Design, 1989

1988
A comparative study on some methods for computing equilibrium concentrations.
Computers & Chemistry, 1988

1987
A general method for the determination of the stoichiometry of unknown species in multicomponent systems from physicochemical measurements.
Computers & Chemistry, 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.
Computers & Chemistry, 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.
Computers & Chemistry, 1984


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