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List of works by Adam Liwo

A Maximum-Likelihood Approach to Force-Field Calibration.

scientific article published on 11 August 2015

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

scientific article published in March 2017

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains

scientific article published in September 2017

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and f

scientific article published on 01 April 2019

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

scientific article

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

scientific article published on 11 October 2018

A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28))

scientific article published on 18 October 2011

A theoretical study of glucosamine synthase. II. Combined quantum and molecular mechanics simulation of sulfhydryl attack on the carboxyamide group

scientific article published on 01 January 1992

A theoretical study of the mechanism of oxygen binding by model anthraquinones. I: Quantum mechanical evaluation of the oxygen-binding sites of 1,4-hydroquinone

scientific article published on 01 December 1992

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions

scientific article

A united residue force-field for calcium-protein interactions.

scientific article

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

scientific article

Ab initio study of the mechanism of singlet-dioxygen addition to hydroxyaromatic compounds: negative evidence for the involvement of peroxa and endoperoxide intermediates.

scientific article

Accounting for a mirror-image conformation as a subtle effect in protein folding

scientific article

Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment

scientific article

Addition of side chains to a known backbone with defined side-chain centroids

scientific article published in January 2003

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

scientific article

An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.

scientific article

Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction

scientific article published on 10 October 2019

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins

scientific article published on March 2009

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

scientific article published on 07 October 2019

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

scientific article published on 03 January 2020

Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment

scientific article published on March 2006

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

CAS MCSCF/CAS MCQDPT2 Study of the Mechanism of Singlet Oxygen Addition to 1,3-Butadiene and Benzene

article

Coarse-Grained Models of Proteins: Theory and Applications

Coarse-grained force field: general folding theory

scientific article

Coarse-grained model of nucleic acid bases

scientific article published in June 2010

Coexistence of phases in a protein heterodimer

scientific article

Combination of SAXS and NMR Techniques as a Tool for the Determination of Peptide Structure in Solution

article published in 2010

Common functionally important motions of the nucleotide-binding domain of Hsp70

scientific article

Computational techniques for efficient conformational sampling of proteins

scientific article published on 22 January 2008

Conformational Aspects of Differences in Requirements for Oxytocin and Vasopressin Receptors

scientific article published on 01 January 1995

Conformational Dynamics of the Trp-Cage Miniprotein at Its Folding Temperature

article

Conformational solution studies of neuropeptide gamma using CD and NMR spectroscopy.

scientific article published in May 2002

Conformational studies of cyclic enkephalin analogues with L- or D-proline in position 3.

scientific article published in April 2002

Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus

scientific article

Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.

scientific article

Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

scientific article published on 28 December 2017

Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides.

scientific article published in December 1996

DNA Duplex Formation with a Coarse-Grained Model

scientific article

Design of a knowledge-based force field for off-lattice simulations of protein structure

scientific article published on January 1, 1997

Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine

scientific article

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.

scientific article published on 01 April 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

scientific article

Determination of the Potentials of Mean Force for Rotation about Cα−CαVirtual Bonds in Polypeptides from the ab Initio Energy Surfaces of Terminally Blocked Glycine, Alanine, and Proline†

Determination of the pKa values of some biologically active and inactive hydroxyquinones

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

article

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A.

scientific article

Dynamics study on single and multiple β-sheets

article

Effects of compact volume and chain stiffness on the conformations of native proteins ⬇️

scientific article published on July 15, 1992

Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain

scientific article published on 2 May 2012

Electrochemical and UV-spectrophotometric study of oxygen and superoxide anion radical interaction with anthraquinone derivatives and their radical anions

article published in 2000

Electrochemical studies of isolapachol with emphasis on oxygen interaction with its radical anions

Electrochemical study of oxygen interaction with lapachol and its radical anions.

scientific article published in April 2003

Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method

scientific article published on 01 May 2002

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins

scientific article

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment

scientific article published on 26 July 2019

Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein

scientific article

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins

scientific article published on 01 January 2002

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field

scientific article published on October 2009

Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues

scientific article

Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer

scientific article published on 10 September 2019

Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins

scientific article published on 01 February 2020

Folding and self-assembly of a small protein complex

scientific article published on September 2012

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

scientific article

Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope

scientific article published on 01 January 2019

Further evidence for the absence of polyproline II stretch in the XAO peptide.

scientific article

Hidden protein folding pathways in free-energy landscapes uncovered by network analysis

scientific article

How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?

scientific article published on 12 June 2009

Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models

scientific article published on 01 February 2020

Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase.

scientific article published on 20 April 2018

Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field

scientific article published on August 2008

Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function

scientific article published in November 2006

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

scientific article

Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain

scientific article published on June 2008

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13

scientific article published on 11 February 2020

Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

article published in 2004

Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.

scientific article

In situ data analytics and indexing of protein trajectories

scientific article

Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides

scientific article

Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5).

scientific article

Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners

scientific article published in Scientific Reports

Interplay of charge distribution and conformation in peptides: comparison of theory and experiment

scientific article published in January 2005

Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes

scientific article published on 26 June 2019

Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints

scientific article published on 29 April 2019

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

scientific article

Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains

scientific article published on 10 November 2005

Kinks, loops, and protein folding, with protein A as an example

scientific article

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

scientific article

Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal

scientific article

Local and long range potentials for heparin-protein systems for coarse-grained simulations

scientific article published on 13 March 2019

Local vs global motions in protein folding

scientific article published on July 2013

MCSCF study of singlet oxygen addition to ethenol?a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups

article

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

scientific article published on 15 August 2017

Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix

scientific article published in Physical Review Letters

Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field

scientific article

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure

scientific article

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation

scientific article published on August 2009

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions

scientific article published on February 2010

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein

scientific article

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

scientific article

Molecular determinants of singlet oxygen binding by anthraquinones in relation to their redox cycling activity

scientific article published on November 1, 1991

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

scientific article

Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate.

scientific article published in January 2003

Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides

scientific article

Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins

scientific article published on January 2007

Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

scientific article published on July 2005

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

scientific article published on July 2005

Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

scientific article published on 6 June 2015

Molecular origin of anticooperativity in hydrophobic association

scientific article published on 01 April 2005

Molecular simulation study of cooperativity in hydrophobic association

scientific article published in June 2000

Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles

scientific article published on 01 September 2003

Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides

scientific article published in January 2012

New developments of the electrostatically driven monte carlo method: Test on the membrane-bound portion of melittin ⬇️

scientific article published on August 1, 1998

Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

scientific article

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins

article

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization

article by Stanislaw Oldziej et al published October 2004 in Journal of Physical Chemistry

PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics

scientific article

Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems†

article

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

scientific article

Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions

scientific article published on January 2015

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations

scientific article

Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.

scholarly article

Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit.

scientific article

Potential of mean force of hydrophobic association: dependence on solute size.

scientific article published on 22 August 2007

Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing

scientific article published on 01 July 2018

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.

scientific article

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information

scientific article published on 14 November 2017

Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

scientific article

Principal component analysis for protein folding dynamics

scientific article published on 15 October 2008

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

scientific article

Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems

scientific article published on 08 August 2018

Pseudopotentials for coarse‐grained cross‐link‐assisted modeling of protein structures

scientific article published on 17 August 2021

Recent Developments in Data-Assisted Modeling of Flexible Proteins

publication published on 24 December 2021

Relation between free energy landscapes of proteins and dynamics

scientific article published on February 2010

Reoptimized UNRES Potential for Protein Model Quality Assessment

article

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

scientific article

Role of the sulfur to α-carbon thioether bridges in thurincin H.

scientific article published on 11 September 2016

Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers

scientific article published on 24 February 2020

Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone

scientific article published in October 2007

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains

article

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains

scientific article published on 21 December 2016

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model

scientific article published on 27 February 2007

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems

scientific article published on 27 February 2007

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains

scientific article published on 14 August 2008

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains

scientific article

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains

scientific article

Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics

scientific article

Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field

scientific article published on 3 March 2015

The molecular mechanism of structural changes in the antimicrobial peptide CM15 upon complex formation with drug molecule suramin: a computational analysis

scientific article published on 13 May 2019

The photophysics of β-homo-tyrosine and its simple derivatives

scientific article published in December 1996

The role of the Val57 amino-acid residue in the hinge loop of the human cystatin C. Conformational studies of the beta2-L1-beta3 segments of wild-type human cystatin C and its mutants

scientific article published in May 2009

Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water

scientific article

Theoretical and electrochemical study of the mechanism of anthraquinone-mediated one-electron reduction of oxygen: the involvement of adducts of dioxygen species to anthraquinones

article

Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force.

scientific article published in February 2005

Theoretical conformational analysis of three vasopressin antagonists with a modified cyclohexyl ring in the first thioacid residue ⬇️

scientific article published on 01 May 1995

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

scientific article published on 01 September 1989

Theoretical study of the energetics of the reactions of triplet dioxygen with hydroquinone, semiquinone, and their protonated forms: relation to the mechanism of superoxide generation in the respiratory chain

scientific article published on 14 March 2007

Theoretical study of the role of hydrogen bonding and proton transfer in oxygen reduction by semiquinones

Topology of Type II REases revisited; structural classes and the common conserved core

scientific article

Toward temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. II. Molecular dynamics study of pairs of different types of interactions in water at various temperatures

scientific article

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations

Towards gelsolin amyloid formation

scientific article published on 01 January 2004

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.

scientific article

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

scientific article published in July 2018

UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations

scientific article published on 18 October 2020

Unfolding the prospects of computational (bio)materials modeling

scientific article published on 01 September 2020

Use of NMR and fluorescence spectroscopy as well as theoretical conformational analysis in conformation-activity studies of cyclic enkephalin analogues

scientific article published on January 2004

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

scientific article

Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets

scientific article published on 24 May 2018

WeFold: a coopetition for protein structure prediction

scientific article

beta-hairpin-forming peptides; models of early stages of protein folding

scientific article

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