List of works - Stanislaw Oldziej

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

scientific article

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

scientific article

Azapeptides structurally based upon inhibitory sites of cystatins as potent and selective inhibitors of cysteine proteases.

scientific article

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

article

Chelating ability and biological activity of hesperetin Schiff base.

scientific article

Coarse-Grained Models of Proteins: Theory and Applications

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

article published in 2010

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 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

Coordination ability of pentapeptides with two dehydro-amino acid residues inserted into their sequences

scientific article published on 01 August 2004

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

scientific article published on 28 December 2017

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†

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

article

Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin

scientific article

Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field.

scientific article

Effect of tetrazole moiety on coordinating efficiency of deltorphin

scientific article published in January 2004

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

scientific article

Fluorescence study of neurohypophyseal hormones and their analogues

scientific article published on 01 January 1997

Human follicular fluid proteomic and peptidomic composition quantitative studies by SWATH-MS methodology. Applicability of high pH RP-HPLC fractionation.

scientific article published on 9 March 2018

Impact of 1,5-disubstituted tetrazole ring on chelating ability of delta-selective opioid peptide

scientific article

Impact of histidine residue on chelating ability of 2′-deoxyriboadenosine

scientific article published on 27 May 2011

Impact of ring size on the copper(II) coordination abilities of cyclic tetrapeptides.

scientific article

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

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

Investigation of the inhibition pathway of glucosamine synthase by N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid by semiempirical quantum mechanical and molecular mechanics methods.

scientific article published in January 1992

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

scientific article

MNDO study of the mechanism of the inhibition of cysteine proteinases by diazomethyl ketones.

scientific article published in January 1992

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 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

Molecular modeling of the catalytic domain of serine/threonine phosphatase-1 with the Zn2+ and Mn2+ di-nuclear ion centers in the active site

scientific article published on 01 May 2000

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

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

Photophysical properties ofβ-homo-tyrosine derivatives

scientific article published on 01 June 1996

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

scientific article published on 22 August 2007

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

scientific article

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.

scientific article

Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC-MS and SWATH Methodology.

scientific article

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

scientific article

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 for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains

scientific article published on 14 August 2008

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

scientific article

The copper(II) coordination abilities of three novel cyclic tetrapeptides with -His-Xaa-His- motif

scientific article published on 21 November 2006

The influence of the cyclopeptide sequence on its coordination abilities towards Cu(II)

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

scientific article published in December 1996

The unusual stabilization of the Ni2+ and Cu2+ complexes with NSFRY.

scientific article published on 22 October 2012

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

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 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

Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box Interactions

scientific article

Unusual gain in the coordination ability of vasopressin-like peptides towards Cu2+ ions by insertion of the highly hydrophobic side chain

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

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

scientific article

List of works by Stanislaw Oldziej

A Maximum-Likelihood Approach to Force-Field Calibration.

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

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

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

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

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

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

Azapeptides structurally based upon inhibitory sites of cystatins as potent and selective inhibitors of cysteine proteases.

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

Chelating ability and biological activity of hesperetin Schiff base.

Coarse-Grained Models of Proteins: Theory and Applications

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

Computational techniques for efficient conformational sampling of proteins

Conformational Aspects of Differences in Requirements for Oxytocin and Vasopressin Receptors

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

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

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

Coordination ability of pentapeptides with two dehydro-amino acid residues inserted into their sequences

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

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†

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

Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin

Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field.

Effect of tetrazole moiety on coordinating efficiency of deltorphin

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

Fluorescence study of neurohypophyseal hormones and their analogues

Human follicular fluid proteomic and peptidomic composition quantitative studies by SWATH-MS methodology. Applicability of high pH RP-HPLC fractionation.

Impact of 1,5-disubstituted tetrazole ring on chelating ability of delta-selective opioid peptide

Impact of histidine residue on chelating ability of 2′-deoxyriboadenosine

Impact of ring size on the copper(II) coordination abilities of cyclic tetrapeptides.

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.

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

Investigation of the inhibition pathway of glucosamine synthase by N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid by semiempirical quantum mechanical and molecular mechanics methods.

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

MNDO study of the mechanism of the inhibition of cysteine proteinases by diazomethyl ketones.

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

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

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

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

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

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

Molecular modeling of the catalytic domain of serine/threonine phosphatase-1 with the Zn2+ and Mn2+ di-nuclear ion centers in the active site

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

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

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

Photophysical properties ofβ-homo-tyrosine derivatives

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

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

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.

Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC-MS and SWATH Methodology.

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

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

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

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

The copper(II) coordination abilities of three novel cyclic tetrapeptides with -His-Xaa-His- motif

The influence of the cyclopeptide sequence on its coordination abilities towards Cu(II)

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

The unusual stabilization of the Ni2+ and Cu2+ complexes with NSFRY.

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

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

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

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.

Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box Interactions

Unusual gain in the coordination ability of vasopressin-like peptides towards Cu2+ ions by insertion of the highly hydrophobic side chain

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

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