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Journal Articles

Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate

Hongnan Cao, Jeffrey Skolnick

Struct. Dyn. 6, 024701 (2019)

https://doi.org/10.1063/1.5086436

Published: March 2019

View articletitled, Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate

Includes: Supplementary data

Journal Articles

Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

Jeffrey Skolnick

J. Chem. Phys. 145, 100901 (2016)

https://doi.org/10.1063/1.4962258

Published: September 2016

View articletitled, Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

Journal Articles

Are protein-protein interfaces special regions on a protein’s surface?

Sam Tonddast-Navaei, Jeffrey Skolnick

J. Chem. Phys. 143, 243149 (2015)

https://doi.org/10.1063/1.4937428

Published: December 2015

View articletitled, Are protein-protein interfaces special regions on a protein’s surface?

Includes: Supplementary data

Journal Articles

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

Tadashi Ando, Edmond Chow, Jeffrey Skolnick

J. Chem. Phys. 139, 121922 (2013)

https://doi.org/10.1063/1.4817660

Published: August 2013

View articletitled, Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

Journal Articles

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

Tadashi Ando, Edmond Chow, Yousef Saad, Jeffrey Skolnick

J. Chem. Phys. 137, 064106 (2012)

https://doi.org/10.1063/1.4742347

Published: August 2012

View articletitled, Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

Journal Articles

Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures

Yang Zhang, Jeffrey Skolnick

J. Chem. Phys. 115, 5027–5032 (2001)

https://doi.org/10.1063/1.1396672

Published: September 2001

View articletitled, Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures

Journal Articles

A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics

Dominik Gront, Andrzej Kolinski, Jeffrey Skolnick

J. Chem. Phys. 115, 1569–1574 (2001)

https://doi.org/10.1063/1.1381062

Published: July 2001

View articletitled, A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics

Journal Articles

Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures

Dominik Gront, Andrzej Kolinski, Jeffrey Skolnick

J. Chem. Phys. 113, 5065–5071 (2000)

https://doi.org/10.1063/1.1289533

Published: September 2000

View articletitled, Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures

Journal Articles

Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins

Andrzej Kolinski, Wojciech Galazka, Jeffrey Skolnick

J. Chem. Phys. 108, 2608–2617 (1998)

https://doi.org/10.1063/1.475646

Published: February 1998

View articletitled, Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins

Journal Articles

Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions

Andrzej Kolinski, Jeffrey Skolnick

J. Chem. Phys. 107, 953–964 (1997)

https://doi.org/10.1063/1.474448

Published: July 1997

View articletitled, Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions

Includes: Supplementary data

Journal Articles

Computer design of idealized β‐motifs

Andrzej Kolinski, Wojciech Galazka, Jeffrey Skolnick

J. Chem. Phys. 103, 10286–10297 (1995)

https://doi.org/10.1063/1.469930

Published: December 1995

View articletitled, Computer design of idealized β‐motifs

Journal Articles

A reduced model of short range interactions in polypeptide chains

Andrzej Kolinski, Mariusz Milik, Jakub Rycombel, Jeffrey Skolnick

J. Chem. Phys. 103, 4312–4323 (1995)

https://doi.org/10.1063/1.470670

Published: September 1995

View articletitled, A reduced model of short range interactions in polypeptide chains

Journal Articles

A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations

Michal Vieth, Andrzej Kolinski, Jeffrey Skolnick

J. Chem. Phys. 102, 6189–6193 (1995)

https://doi.org/10.1063/1.469063

Published: April 1995

View articletitled, A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations

Journal Articles

Computer simulation of the folding of coiled coils

Antonio Rey, Jeffrey Skolnick

J. Chem. Phys. 100, 2267–2276 (1994)

https://doi.org/10.1063/1.466525

Published: February 1994

View articletitled, Computer simulation of the folding of coiled coils

Journal Articles

A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids

Yehudi K. Levine, Andrzej Kolinski, Jeffrey Skolnick

J. Chem. Phys. 98, 7581–7587 (1993)

https://doi.org/10.1063/1.464698

Published: May 1993

View articletitled, A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids

Journal Articles

A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins

Andrzej Kolinski, Adam Godzik, Jeffrey Skolnick

J. Chem. Phys. 98, 7420–7433 (1993)

https://doi.org/10.1063/1.464706

Published: May 1993

View articletitled, A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins

Journal Articles

Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides

Andrzej Kolinski, Jeffrey Skolnick

J. Chem. Phys. 97, 9412–9426 (1992)

https://doi.org/10.1063/1.463317

Published: December 1992

View articletitled, Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides

Journal Articles

Effect of double bonds on the dynamics of hydrocarbon chains

Antonio Rey, Andrzej Kolinski, Jeffrey Skolnick, Yehudi K. Levine

J. Chem. Phys. 97, 1240–1249 (1992)

https://doi.org/10.1063/1.463250

Published: July 1992

View articletitled, Effect of double bonds on the dynamics of hydrocarbon chains

Journal Articles

Static and dynamic properties of a new lattice model of polypeptide chains

Andrzej Kolinski, Mariusz Milik, Jeffrey Skolnick

J. Chem. Phys. 94, 3978–3985 (1991)

https://doi.org/10.1063/1.460675

Published: March 1991

View articletitled, Static and dynamic properties of a new lattice model of polypeptide chains

Journal Articles

Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model

Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick

J. Chem. Phys. 93, 4440–4446 (1990)

https://doi.org/10.1063/1.458726

Published: September 1990

View articletitled, Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model

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Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate

Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

Are protein-protein interfaces special regions on a protein’s surface?

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures

A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics

Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures

Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins

Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions

Computer design of idealized β‐motifs

A reduced model of short range interactions in polypeptide chains

A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations

Computer simulation of the folding of coiled coils

A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids

A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins

Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides

Effect of double bonds on the dynamics of hydrocarbon chains

Static and dynamic properties of a new lattice model of polypeptide chains

Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model

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