List of works - Stanislaw Oldziej

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

scientific article

Computational techniques for efficient conformational sampling of proteins

scientific article published on 22 January 2008

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

scientific article

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

scientific article

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

scientific article published in Physical Review Letters

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

scientific article

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

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

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

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

scientific article

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

article

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

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

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

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

scientific article

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

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

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

scientific article published on 22 August 2007

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

article

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

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

scientific article

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

scientific article

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

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

article

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

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

A Maximum-Likelihood Approach to Force-Field Calibration.

scientific article published on 11 August 2015

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

scientific article published on 15 August 2017

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

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

scientific article

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

scientific article published on 21 November 2006

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†

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

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

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

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

A united residue force-field for calcium-protein interactions

scientific article

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

scientific article published on 22 October 2012

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

scientific article

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

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

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

scientific article

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

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

article published in 2010

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

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

Conformational Aspects of Differences in Requirements for Oxytocin and Vasopressin Receptors

scientific article published on 01 January 1995

List of works by Stanislaw Oldziej

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

Computational techniques for efficient conformational sampling of proteins

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

A Maximum-Likelihood Approach to Force-Field Calibration.

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

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

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

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

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†

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

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

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

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

A united residue force-field for calcium-protein interactions

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

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

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

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

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

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

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

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

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

Conformational Aspects of Differences in Requirements for Oxytocin and Vasopressin Receptors

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