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Lista de obras de Adam Liwo

A Maximum-Likelihood Approach to Force-Field Calibration.

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 2002

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))

artículo científico publicado en 2011

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

artículo científico publicado el 1 de enero de 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

artículo científico publicado el 1 de diciembre de 1992

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

artículo científico publicado en 2014

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

artículo científico publicado en 2004

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

artículo científico publicado en 2005

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

artículo científico publicado en 2002

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

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

artículo científico publicado en 2003

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

artículo científico publicado en 2018

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.

artículo científico publicado en 2009

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

artículo científico publicado en 2019

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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2011

Coarse-grained model of nucleic acid bases

artículo científico publicado en 2010

Coexistence of phases in a protein heterodimer

artículo científico publicado en 2012

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

artículo científico publicado en 2014

Computational techniques for efficient conformational sampling of proteins

artículo científico publicado en 2008

Conformational Aspects of Differences in Requirements for Oxytocin and Vasopressin Receptors

artículo científico publicado en 1995

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

article

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

artículo científico publicado en 2002

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

artículo científico publicado en 2002

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

artículo científico publicado en 2009

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

artículo científico publicado en 2008

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

artículo científico publicado en 2017

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

artículo científico publicado en 1996

DNA Duplex Formation with a Coarse-Grained Model

artículo científico publicado en 2014

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

artículo científico publicado el 1 de enero de 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

artículo científico publicado en 2012

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.

artículo científico publicado en 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

artículo científico publicado en 2010

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.

artículo científico publicado en 2017

Dynamics study on single and multiple β-sheets

article

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

artículo científico publicado el 15 de julio de 1992

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

artículo científico publicado en 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.

artículo científico publicado en 2003

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

artículo científico publicado en 2002

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

artículo científico publicado en 2017

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

artículo científico publicado en 2019

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

artículo científico publicado en 2010

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

artículo científico publicado en 2002

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

artículo científico publicado en 2009

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

artículo científico publicado en 2012

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

artículo científico publicado en 2012

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

artículo científico publicado en 2014

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

artículo científico publicado en 2019

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

artículo científico publicado en 2007

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

artículo científico publicado en 2012

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

artículo científico publicado en 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.

artículo científico publicado en 2018

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

artículo científico publicado en 2008

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

artículo científico publicado en 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.

artículo científico publicado en 2010

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

artículo científico publicado en 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.

artículo científico publicado en 2013

In situ data analytics and indexing of protein trajectories

artículo científico publicado en 2017

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

artículo científico publicado en 2008

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).

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado en 2005

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2010

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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2010

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.

artículo científico publicado en 2007

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

artículo científico publicado el 1 de noviembre de 1991

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

artículo científico publicado en 2016

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

artículo científico publicado en 2003

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

artículo científico publicado en 2006

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

artículo científico publicado en 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

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2015

Molecular origin of anticooperativity in hydrophobic association

artículo científico publicado en 2005

Molecular simulation study of cooperativity in hydrophobic association

artículo científico publicado en 2000

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

artículo científico publicado en 2003

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

artículo científico publicado en 2012

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

artículo científico publicado el 1 de agosto de 1998

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

artículo científico publicado en 2015

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

artículo científico publicado en 2010

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.

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2006

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

artículo científico publicado en 2010

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

artículo científico publicado en 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.

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2004

Principal component analysis for protein folding dynamics

artículo científico publicado en 2008

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

artículo científico publicado en 2007

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2011

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

artículo científico publicado en 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2019

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 2015

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.

artículo científico publicado en 2005

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

artículo científico publicado el 1 de mayo de 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2007

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

artículo científico publicado en 2012

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.

artículo científico publicado en 2009

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

artículo científico publicado en 2018

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

artículo científico publicado en 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

artículo científico publicado en 2004

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

WeFold: a coopetition for protein structure prediction

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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