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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

The journal of physical chemistry. B, 2007-01, Vol.111 (1), p.260-285

2007

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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size

The journal of physical chemistry. B, 2007-09, Vol.111 (36), p.10765-10774

2007

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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

The journal of physical chemistry. B, 2008-09, Vol.112 (36), p.11385-11395

2008

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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 force-field calibration and validation

The Journal of chemical physics, 2019-04, Vol.150 (15), p.155104-155104

2019

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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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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

The journal of physical chemistry. B, 2007-03, Vol.111 (11), p.2925-2931

2007

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

Proteins, structure, function, and bioinformatics, 2010-02, Vol.78 (3), p.723-737

2010

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Follicular Fluid Proteomic Analysis to Identify Predictive Markers of Normal Embryonic Development

International journal of molecular sciences, 2024-08, Vol.25 (15), p.8431

2024

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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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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2376, p.399

2022

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

Journal of chemical information and modeling, 2017-09, Vol.57 (9), p.2364-2377

2017

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Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples

International journal of molecular sciences, 2024-08, Vol.25 (16), p.8799

2024

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

Biopolymers, 2009-01, Vol.91 (1), p.37-51

2009

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

The journal of physical chemistry. B, 2012-06, Vol.116 (23), p.6898-6907

2012

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

Physical review letters, 2013-02, Vol.110 (9), p.098101-098101, Article 098101

2013

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

Journal of molecular modeling, 2014-08, Vol.20 (8), p.2306-2306, Article 2306

2014

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

Journal of chemical information and modeling, 2018-01, Vol.58 (1), p.206-206

2018

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Compatibility of Distinct Label-Free Proteomic Workflows in Absolute Quantification of Proteins Linked to the Oocyte Quality in Human Follicular Fluid

International journal of molecular sciences, 2021-07, Vol.22 (14), p.7415

2021

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

Journal of proteome research, 2017-08, Vol.16 (8), p.3053-3067

2017

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Computational techniques for efficient conformational sampling of proteins

Current opinion in structural biology, 2008-04, Vol.18 (2), p.134-139

2008

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Substitutions at position 263 within the von Willebrand factor type A domain determine the functionality of complement C2 protein

Frontiers in immunology, 2022-12, Vol.13, p.1061696-1061696

2022

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AfsK-Mediated Site-Specific Phosphorylation Regulates DnaA Initiator Protein Activity in Streptomyces coelicolor

Journal of bacteriology, 2020-01, Vol.202 (3)

2020

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

Biopolymers, 2010-05, Vol.93 (5), p.469-480

2010

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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

Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size

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

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 force-field calibration and validation

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

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

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. 2. Off-Lattice Tests of the Method with Single Proteins

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

Follicular Fluid Proteomic Analysis to Identify Predictive Markers of Normal Embryonic Development

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

Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

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

Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples

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

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

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

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

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

Compatibility of Distinct Label-Free Proteomic Workflows in Absolute Quantification of Proteins Linked to the Oocyte Quality in Human Follicular Fluid

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

Computational techniques for efficient conformational sampling of proteins

Substitutions at position 263 within the von Willebrand factor type A domain determine the functionality of complement C2 protein

AfsK-Mediated Site-Specific Phosphorylation Regulates DnaA Initiator Protein Activity in Streptomyces coelicolor

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

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