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Efficient calculation of rate constants: downhill versus uphill sampling

The Journal of chemical physics, 2014-08, Vol.141 (7), p.074103-074103

Klenin, Konstantin V

2014

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Derivatives of molecular surface area and volume: Simple and exact analytical formulas

Journal of computational chemistry, 2011-09, Vol.32 (12), p.2647-2653

2011

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Calculation of the "absolute" free energy of a β-hairpin in an all-atom force field

The Journal of chemical physics, 2013-08, Vol.139 (5), p.054102-054102

2013

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Transition network based on equilibrium sampling: A new method for extracting kinetic information from Monte Carlo simulations of protein folding

The Journal of chemical physics, 2011-12, Vol.135 (23), p.235105-235105-10

2011

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Computation of writhe in modeling of supercoiled DNA

Biopolymers, 2000-10, Vol.54 (5), p.307-317

2000

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A method for the calculation of rate constants from stochastic transition paths

The Journal of chemical physics, 2010-03, Vol.132 (10), p.104104-104104

2010

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Facilitated diffusion of DNA-binding proteins

Physical review letters, 2006-01, Vol.96 (1), p.018104-018104, Article 018104

2006

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Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition

PloS one, 2009-11, Vol.4 (11), p.e7756-e7756

2009

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Kinetics of protein binding in solid-phase immunoassays: theory

The Journal of chemical physics, 2005-06, Vol.122 (21), p.214715-214715

2005

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Modeling of intramolecular reactions of polymers: an efficient method based on Brownian dynamics simulations

The Journal of chemical physics, 2004-09, Vol.121 (10), p.4951-4960

2004

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Facilitated diffusion of DNA-binding proteins: Simulation of large systems

The Journal of chemical physics, 2006-07, Vol.125 (1), p.014906-014906-8

2006

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Facilitated diffusion of DNA-binding proteins: efficient simulation with the method of excess collisions

The Journal of chemical physics, 2006-04, Vol.124 (13), p.134908-134908

2006

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Calculation of the "absolute" free energy of a ?-hairpin in an all-atom force field

The Journal of chemical physics, 2013-01, Vol.139 (5)

2013

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Intrachain Reactions of Supercoiled DNA Simulated by Brownian Dynamics

Biophysical journal, 2001-10, Vol.81 (4), p.1924-1929

2001

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Diffusion-Controlled Intrachain Reactions of Supercoiled DNA: Brownian Dynamics Simulations

Biophysical journal, 2001, Vol.80 (1), p.69-74

2001

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Branched DNA That Forms a Solid at 95 °C

Angewandte Chemie (International ed.), 2011-03, Vol.50 (14), p.3227-3231

International ed. in English, 2011

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Conformational and thermodynamic properties of supercoiled DNA

Journal of molecular biology, 1992-10, Vol.227 (4), p.1224-1243

1992

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A method for the calculation of rate constants from stochastictransition paths

The Journal of chemical physics, 2010-03, Vol.132 (10), p.104104-104104-5

2010

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Modelling proteins: Conformational sampling and reconstruction of folding kinetics

Biochimica et biophysica acta, 2011-08, Vol.1814 (8), p.977-1000

2011

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Template‐free protein structure prediction and quality assessment with an all‐atom free‐energy model

Proteins, structure, function, and bioinformatics, 2009-11, Vol.77 (2), p.330-341

2009

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Probing hot spots on protein-protein interfaces with all-atom free-energy simulation

The Journal of chemical physics, 2009-07, Vol.131 (3), p.034114-034114-11

2009

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Kinetics of antigen binding to antibody microspots: Strong limitation by mass transport to the surface

Proteomics (Weinheim), 2006-02, Vol.6 (3), p.794-803

2006

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All Atom Protein Folding Simulations With Distributed Computational Resources

Biophysical journal, 2009-02, Vol.96 (3), p.592a-592a

2009

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Performance of An All-Atom Free Energy Approach For Protein Structure Prediction

Biophysical journal, 2011-02, Vol.100 (3), p.48a-48a

2011

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A Brownian Dynamics Program for the Simulation of Linear and Circular DNA and Other Wormlike Chain Polyelectrolytes

Biophysical journal, 1998-02, Vol.74 (2), p.780-788

1998

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Efficient calculation of rate constants: downhill versus uphill sampling

Derivatives of molecular surface area and volume: Simple and exact analytical formulas

Calculation of the "absolute" free energy of a β-hairpin in an all-atom force field

Transition network based on equilibrium sampling: A new method for extracting kinetic information from Monte Carlo simulations of protein folding

Computation of writhe in modeling of supercoiled DNA

A method for the calculation of rate constants from stochastic transition paths

Facilitated diffusion of DNA-binding proteins

Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition

Kinetics of protein binding in solid-phase immunoassays: theory

Modeling of intramolecular reactions of polymers: an efficient method based on Brownian dynamics simulations

Facilitated diffusion of DNA-binding proteins: Simulation of large systems

Facilitated diffusion of DNA-binding proteins: efficient simulation with the method of excess collisions

Calculation of the "absolute" free energy of a ?-hairpin in an all-atom force field

Intrachain Reactions of Supercoiled DNA Simulated by Brownian Dynamics

Diffusion-Controlled Intrachain Reactions of Supercoiled DNA: Brownian Dynamics Simulations

Branched DNA That Forms a Solid at 95 °C

Conformational and thermodynamic properties of supercoiled DNA

A method for the calculation of rate constants from stochastictransition paths

Modelling proteins: Conformational sampling and reconstruction of folding kinetics

Template‐free protein structure prediction and quality assessment with an all‐atom free‐energy model

Probing hot spots on protein-protein interfaces with all-atom free-energy simulation

Kinetics of antigen binding to antibody microspots: Strong limitation by mass transport to the surface

All Atom Protein Folding Simulations With Distributed Computational Resources

Performance of An All-Atom Free Energy Approach For Protein Structure Prediction

A Brownian Dynamics Program for the Simulation of Linear and Circular DNA and Other Wormlike Chain Polyelectrolytes

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