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A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance

Frontiers in immunology, 2022-03, Vol.13, p.816634

2022

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Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin

The journal of physical chemistry. B, 2012-07, Vol.116 (29), p.8584-8603

2012

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Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

The Journal of chemical physics, 2011-02, Vol.134 (8), p.085103-085103-25

2011

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Optical Interference Lithography Using Azobenzene-Functionalized Polymers for Micro- and Nanopatterning of Silicon

Advanced materials (Weinheim), 2011-09, Vol.23 (36), p.4174-4177

2011

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QM/MM free energy simulations: recent progress and challenges

Molecular simulation, 2016-09, Vol.42 (13), p.1056-1078

2016

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Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

eLife, 2018-02, Vol.7

2018

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Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin

Biochemistry (Easton), 2017-03, Vol.56 (10), p.1482-1497

2017

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The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

Nature communications, 2020-09, Vol.11 (1), p.4437-4437, Article 4437

2020

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Reflection from Disordered Silver Nanoparticles on Multilayer Substrate

Sensors & transducers, 2015-10, Vol.193 (10), p.170-170

Ovchinnikov, Victor

2015

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Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV‑2 Spike Indicate a Barrierless Transition with Slow Conformational Motions

The journal of physical chemistry. B, 2023-10, Vol.127 (40), p.8565-8575

2023

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Numerical simulations of boundary-layer bypass transition due to high-amplitude free-stream turbulence

Journal of fluid mechanics, 2008-10, Vol.613, p.135-169

2008

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On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

Antibodies (Basel), 2022-08, Vol.11 (3), p.51

2022

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Fatigue Resistance of 01420 S Alloy Welded Joints Made by Various Welding Methods

MATEC Web of Conferences, 2021, Vol.346, p.1013

2021

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Mechanical Coupling in Myosin V: A Simulation Study

Journal of molecular biology, 2010-01, Vol.395 (4), p.815-833

2010

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Photolithographic periodic patterning of gold using azobenzene-functionalized polymers

Thin solid films, 2013-07, Vol.540, p.162-167

2013

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Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway

The journal of physical chemistry. B, 2023-07, Vol.127 (26), p.5789-5798

2023

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ppdx: Automated modeling of protein–protein interaction descriptors for use with machine learning

Journal of computational chemistry, 2022-09, Vol.43 (25), p.1747-1757

2022

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Self-Organization-Based Fabrication of Stable Noble-Metal Nanostructures on Large-Area Dielectric Substrates

Journal of chemistry, 2013-01, Vol.2013 (1)

2013

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A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems

The Journal of chemical physics, 2020-09, Vol.153 (12), p.121103-121103

2020

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Molecular Simulation of Stapled Peptides

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2405, p.283

2022

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A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes

The journal of physical chemistry. B, 2016-08, Vol.120 (33), p.8457-8472

2016

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Structure of the EmrE multidrug transporter and its use for inhibitor peptide design

Proceedings of the National Academy of Sciences - PNAS, 2018-08, Vol.115 (34), p.E7932-E7941

2018

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A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences

The journal of physical chemistry. B, 2013-01, Vol.117 (3), p.750-762

2013

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Changing the Paradigm of Natural Ecosystems Management

Journal of Economic Regulation, 2023-03, Vol.14 (1), p.49-58

2023

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Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase

Journal of the American Chemical Society, 2015-10, Vol.137 (39), p.12454-12457

2015

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A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance

Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

Optical Interference Lithography Using Azobenzene-Functionalized Polymers for Micro- and Nanopatterning of Silicon

QM/MM free energy simulations: recent progress and challenges

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

Reflection from Disordered Silver Nanoparticles on Multilayer Substrate

Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV‑2 Spike Indicate a Barrierless Transition with Slow Conformational Motions

Numerical simulations of boundary-layer bypass transition due to high-amplitude free-stream turbulence

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

Fatigue Resistance of 01420 S Alloy Welded Joints Made by Various Welding Methods

Mechanical Coupling in Myosin V: A Simulation Study

Photolithographic periodic patterning of gold using azobenzene-functionalized polymers

Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway

ppdx: Automated modeling of protein–protein interaction descriptors for use with machine learning

Self-Organization-Based Fabrication of Stable Noble-Metal Nanostructures on Large-Area Dielectric Substrates

A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems

Molecular Simulation of Stapled Peptides

A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes

Structure of the EmrE multidrug transporter and its use for inhibitor peptide design

A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences

Changing the Paradigm of Natural Ecosystems Management

Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase

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