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Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests

Proceedings of the National Academy of Sciences - PNAS, 2005-05, Vol.102 (21), p.7547-7552

2005

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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, 1998-02, Vol.19 (3), p.259-276

1998

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

Journal of chemical theory and computation, 2007-07, Vol.3 (4), p.1236-1248

2007

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Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformational analysis and NMR spectroscopy--application to DNS1-c-[D-A2,bu2,Trp4,Leu5]enkephalin and DNS1-c-[D-A2bu2,Trp4,D-Leu5]enkephalin

Journal of biomolecular NMR, 1999-12, Vol.15 (4), p.315-330

1999

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Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically driven Monte Carlo and molecular dynamics methods

Biopolymers, 1996-02, Vol.38 (2), p.157-175

1996

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Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers

Acta biochimica polonica, 2001-01, Vol.48 (1), p.35-52

2001

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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, 1997-05, Vol.18 (7), p.849-873

1997

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

Protein engineering, design and selection, 2004-01, Vol.17 (1), p.29-36

2004

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Coordination ability of insect kinin analogs

Polyhedron, 2009-02, Vol.28 (3), p.485-492

2009

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Fluorescence study of neurohypophyseal hormones and their analogues. Distance distributions in a series of arginine-vasopressin analogues

European biophysics journal, 1997-01, Vol.26 (2), p.183-193

1997

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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field

Multiscale modeling & simulation, 2006-01, Vol.5 (4), p.1175-1195

2006

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Mechanism of action of aspartic proteinases: application of transition-state analogue theory

Journal of computer-aided molecular design, 1996-12, Vol.10 (6), p.583-588

1996

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Photophysical properties ofβ-homo-tyrosine derivatives

Amino acids, 1996-06, Vol.10 (2), p.197-200

1996

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

Acta biochimica polonica, 1997-01, Vol.44 (3), p.527-547

1997

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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, 1997-05, Vol.18 (7), p.874-887

1997

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The protein folding problem: global optimization of the force fields

Frontiers in bioscience, 2004-09, Vol.9 (1-3), p.3296

2004

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A Method for Optimizing Potential-Energy Functions by a Hierarchical Design of the Potential-Energy Landscape: Application to the UNRES Force Field

Proceedings of the National Academy of Sciences - PNAS, 2002-02, Vol.99 (4), p.1937-1942

2002

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

The journal of physical chemistry. B, 2004-07, Vol.108 (27), p.9421-9438

2004

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Recent Improvements in Prediction of Protein Structure by Global Optimization of a Potential Energy Function

Proceedings of the National Academy of Sciences - PNAS, 2001-02, Vol.98 (5), p.2329-2333

2001

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

The journal of physical chemistry. B, 2004-10, Vol.108 (43), p.16950-16959

2004

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

The journal of physical chemistry. B, 2004-10, Vol.108 (43), p.16934-16949

2004

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

Journal of the American Chemical Society, 2000-08, Vol.122 (34), p.8112-8119

2000

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

Computers & chemistry, 2000-05, Vol.24 (3-4), p.381-390

2000

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

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2003-10, Vol.107 (40), p.8035-8046

2003

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Azapeptides Structurally Based upon Inhibitory Sites of Cystatins as Potent and Selective Inhibitors of Cysteine Proteases

Journal of medicinal chemistry, 2002-09, Vol.45 (19), p.4202-4211

2002

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Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests

United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials

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

Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformational analysis and NMR spectroscopy--application to DNS1-c-[D-A2,bu2,Trp4,Leu5]enkephalin and DNS1-c-[D-A2bu2,Trp4,D-Leu5]enkephalin

Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically driven Monte Carlo and molecular dynamics methods

Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers

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

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

Coordination ability of insect kinin analogs

Fluorescence study of neurohypophyseal hormones and their analogues. Distance distributions in a series of arginine-vasopressin analogues

A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field

Mechanism of action of aspartic proteinases: application of transition-state analogue theory

Photophysical properties ofβ-homo-tyrosine derivatives

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

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

The protein folding problem: global optimization of the force fields

A Method for Optimizing Potential-Energy Functions by a Hierarchical Design of the Potential-Energy Landscape: Application to the UNRES Force Field

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

Recent Improvements in Prediction of Protein Structure by Global Optimization of a Potential Energy Function

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

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

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

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

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

Azapeptides Structurally Based upon Inhibitory Sites of Cystatins as Potent and Selective Inhibitors of Cysteine Proteases

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