Toward accurately modeling N-methylated cyclic peptides

Diana P. Slough; Hongtao Yu; Sean M. McHugh; Yu-Shan Lin

doi:10.1039/c6cp07700e

Toward accurately modeling N-methylated cyclic peptides

Physical Chemistry Chemical Physics ◽

10.1039/c6cp07700e ◽

2017 ◽

Vol 19 (7) ◽

pp. 5377-5388 ◽

Cited By ~ 10

Author(s):

Diana P. Slough ◽

Hongtao Yu ◽

Sean M. McHugh ◽

Yu-Shan Lin

Keyword(s):

Structure Prediction ◽

Cyclic Peptides ◽

Sampling Methods ◽

Enhanced Sampling ◽

Cyclic Hexapeptides

Structure prediction of benchmark N-methylated cyclic hexapeptides using enhanced sampling methods.

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Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c00380 ◽

2021 ◽

Author(s):

Masatake Sugita ◽

Satoshi Sugiyama ◽

Takuya Fujie ◽

Yasushi Yoshikawa ◽

Keisuke Yanagisawa ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Membrane Permeability ◽

Lipid Bilayer ◽

Cyclic Peptides ◽

Large Scale ◽

Enhanced Sampling ◽

Permeability Prediction ◽

Dynamics Simulations

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PyAutoFEP: An Automated Free Energy Perturbation Workflow for GROMACS Integrating Enhanced Sampling Methods

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.1c00194 ◽

2021 ◽

Author(s):

Luan Carvalho Martins ◽

Elio A. Cino ◽

Rafaela Salgado Ferreira

Keyword(s):

Free Energy ◽

Sampling Methods ◽

Free Energy Perturbation ◽

Enhanced Sampling ◽

Energy Perturbation

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ChemInform Abstract: CONFORMATION OF CYCLIC PEPTIDES PART 7, CYCLIC HEXAPEPTIDES CONTAINING THE D-PHE-L-PRO SEQUENCE

Chemischer Informationsdienst ◽

10.1002/chin.197345472 ◽

1973 ◽

Vol 4 (45) ◽

pp. no-no

Author(s):

KENNETH D. KOPPLE ◽

ANITA GO ◽

THOMAS J. SCHAMPER ◽

CRAIG S. WILCOX

Keyword(s):

Cyclic Peptides ◽

Cyclic Hexapeptides

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Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides

Journal of Peptide Research ◽

10.1111/j.1399-3011.2004.00110.x ◽

2004 ◽

Vol 63 (4) ◽

pp. 354-364 ◽

Cited By ~ 13

Author(s):

R.N. Riemann ◽

M. Zacharias

Keyword(s):

Molecular Dynamics ◽

Dihedral Angle ◽

Structure Prediction ◽

Cyclic Peptides

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ChemInform Abstract: STUDIES ON CYCLIC PEPTIDES. 5. CONFORMATION AND INTERACTION WITH SMALL MOLECULES OF CYCLIC HEXAPEPTIDES CONTAINING GLUTAMIC ACID OR ASPARTIC ACID RESIDUE

Chemischer Informationsdienst ◽

10.1002/chin.197645381 ◽

1976 ◽

Vol 7 (45) ◽

pp. no-no

Author(s):

T. SUGIHARA ◽

Y. IMANISHI ◽

T. HIGASHIMURA ◽

Y. SHIMONISHI

Keyword(s):

Glutamic Acid ◽

Small Molecules ◽

Aspartic Acid ◽

Cyclic Peptides ◽

Aspartic Acid Residue ◽

Cyclic Hexapeptides

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Substrate Binding Process and Mechanistic Functioning of Type 1 11β-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods

PLoS ONE ◽

10.1371/journal.pone.0025375 ◽

2011 ◽

Vol 6 (9) ◽

pp. e25375 ◽

Cited By ~ 17

Author(s):

Angelo D. Favia ◽

Matteo Masetti ◽

Maurizio Recanatini ◽

Andrea Cavalli

Keyword(s):

Sampling Methods ◽

Substrate Binding ◽

Hydroxysteroid Dehydrogenase ◽

Enhanced Sampling ◽

Binding Process

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Using Long-Timescale Molecular Dynamics Simulations to Benchmark Enhanced Sampling Methods

Biophysical Journal ◽

10.1016/j.bpj.2014.11.1014 ◽

2015 ◽

Vol 108 (2) ◽

pp. 183a

Author(s):

Albert C. Pan ◽

Thomas M. Weinreich ◽

Stefano Piana ◽

David E. Shaw

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sampling Methods ◽

Enhanced Sampling ◽

Dynamics Simulations

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Enhanced Sampling Methods for Atomistic Simulation of Nucleic Acids

Computational Studies of RNA and DNA ◽

10.1007/978-1-4020-4851-3_6 ◽

2006 ◽

pp. 147-167 ◽

Cited By ~ 1

Author(s):

Catherine Kelso ◽

Carlos Simmerling

Keyword(s):

Nucleic Acids ◽

Atomistic Simulation ◽

Sampling Methods ◽

Enhanced Sampling

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Toward structure prediction of cyclic peptides

Physical Chemistry Chemical Physics ◽

10.1039/c4cp04580g ◽

2015 ◽

Vol 17 (6) ◽

pp. 4210-4219 ◽

Cited By ~ 30

Author(s):

Hongtao Yu ◽

Yu-Shan Lin

Keyword(s):

Structure Prediction ◽

Cyclic Peptides ◽

Computational Method ◽

Structural Description

A computational method to provide a converged structural description for cyclic peptides.

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Conformation of cyclic peptides. VIII. Cyclic hexapeptides containing the L-pro-D-phe sequence

Journal of the American Chemical Society ◽

10.1021/ja00815a046 ◽

1974 ◽

Vol 96 (8) ◽

pp. 2597-2605 ◽

Cited By ~ 53

Author(s):

Kenneth D. Kopple ◽

Thomas J. Schamper ◽

Anita Go

Keyword(s):

Cyclic Peptides ◽

Cyclic Hexapeptides

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