相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Self-Assembled Artificial Ion-Channels toward Natural Selection of Functions
Shao-Ping Zheng et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)
Modeling of Peptides with Classical and Novel Machine Learning Force Fields: A Comparison
David Rosenberger et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach
Nikhil Maroli et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2020)
Highly viscoelastic films at the water/air interface: α-Cyclodextrin with anionic surfactants
Alberto S. Luviano et al.
JOURNAL OF COLLOID AND INTERFACE SCIENCE (2020)
Rings, Hexagons, Petals, and Dipolar Moment Sink-Sources: The Fanciful Behavior of Water around Cyclodextrin Complexes
Pablo F. Garrido et al.
BIOMOLECULES (2020)
Scalable molecular dynamics on CPU and GPU architectures with NAMD
James C. Phillips et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Water in Nanopores and Biological Channels: A Molecular Simulation Perspective
Charlotte Lynch et al.
CHEMICAL REVIEWS (2020)
Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems
Raudah Lazim et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)
Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
Szilard Pall et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Array programming with NumPy
Charles R. Harris et al.
NATURE (2020)
Membrane targeting antimicrobial cyclic peptide nanotubes - an experimental and computational study
Barbara Claro et al.
COLLOIDS AND SURFACES B-BIOINTERFACES (2020)
CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores
Gianni Klesse et al.
JOURNAL OF MOLECULAR BIOLOGY (2019)
Enhanced sampling in molecular dynamics
Yi Isaac Yang et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
Pnina Dauber-Osguthorpe et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2019)
A critical assessment of force field accuracy against NMR data for cyclic peptides containing beta-amino acids
C. Paissoni et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2018)
Developing a molecular dynamics force field for both folded and disordered protein states
Paul Robustelli et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang et al.
NATURE METHODS (2017)
Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface
Angelica Sandoval-Perez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Recent advances in controlling the internal and external properties of self-assembling cyclic peptide nanotubes and dimers
N. Rodriguez-Vazquez et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2017)
Molecular Dynamics Simulations on the Behaviors of Hydrophilic/Hydrophobic Cyclic Peptide Nanotubes at the Water/Hexane Interface
Huifang Lin et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2017)
Parallel and antiparallel cyclic D/L peptide nanotubes
Mitchell R. Silk et al.
CHEMICAL COMMUNICATIONS (2017)
Modelling water molecules inside cyclic peptide nanotubes
Prangsai Tiangtrong et al.
APPLIED NANOSCIENCE (2016)
Lipid Bilayer Membrane Perturbation by Embedded Nanopores: A Simulation Study
Rebeca Garcia-Fandino et al.
ACS NANO (2016)
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik et al.
CHEMICAL REVIEWS (2016)
Computational methods to design cyclic peptides
Sean M. McHugh et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2016)
In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent
Vinodhkumar Vijayakumar et al.
JOURNAL OF MOLECULAR MODELING (2016)
Complex Behavior of Aqueous α-Cyclodextrin Solutions. Interfacial Morphologies Resulting from Bulk Aggregation
Jorge Hernandez-Pascacio et al.
LANGMUIR (2016)
Membrane-Targeted Self-Assembling Cyclic Peptide Nanotubes
Nuria Rodriguez-Vazquez et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2015)
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
Chad W. Hopkins et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Toward structure prediction of cyclic peptides
Hongtao Yu et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2015)
Atomistic organization and characterization of tube-like assemblies comprising peptide-polymer conjugates: computer simulation studies
Oscar Bertran et al.
FARADAY DISCUSSIONS (2013)
An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes
Joakim P. M. Jambeck et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study
Thomas J. Piggot et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
Andreas W. Goetz et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
Kyle A. Beauchamp et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Structure and stability of cyclic peptide based nanotubes: a molecular dynamics study of the influence of amino acid composition
Ramadoss Vijayaraj et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2012)
Systematic Validation of Protein Force Fields against Experimental Data
Kresten Lindorff-Larsen et al.
PLOS ONE (2012)
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
Nathan Schmid et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)
Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations
Naveen Michaud-Agrawal et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data
Oliver F. Lange et al.
BIOPHYSICAL JOURNAL (2010)
A New Force Field for Simulating Phosphatidylcholine Bilayers
David Poger et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations
Jan Domanski et al.
JOURNAL OF MEMBRANE BIOLOGY (2010)
GPU-accelerated molecular modeling coming of age
John E. Stone et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2010)
Molecular Dynamics Simulation for the Structure of the Water Chain in a Transmembrane Peptide Nanotube
Jian Liu et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2010)
On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations
Adil Khalfa et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
Jeffery B. Klauda et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field
Jakob P. Ulmschneider et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Biomolecular simulations of membranes:: Physical properties from different force fields
Shirley W. I. Siu et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
P-LINCS: A parallel linear constraint solver for molecular simulation
Berk Hess
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics
Jingchuan Zhu et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2008)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube
Hyonseok Hwang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers
M Tarek et al.
BIOPHYSICAL JOURNAL (2003)
Atomic weights of the elements:: Review 2000 -: (IUPAC technical report)
JR De Laeter et al.
PURE AND APPLIED CHEMISTRY (2003)
Experimental evidence for the existence of 7H and for a specific structure of 8He -: art. no. 082501
AA Korsheninnikov et al.
PHYSICAL REVIEW LETTERS (2003)
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
GA Kaminski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2001)