Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations

Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations

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Bibliográfalaš dieđut
Váldodahkkit:	Domański, J, Stansfeld, P, Sansom, M, Beckstein, O
Materiálatiipa:	Journal article
Almmustuhtton:	2010

Geahča maid

Lipidbook: a public repository for force-field parameters used in membrane simulations.
Dahkki: Domański, J, et al.
Almmustuhtton: (2010)

Balancing force field protein-lipid interactions to capture transmembrane helix-helix association
Dahkki: Domański, J, et al.
Almmustuhtton: (2018)

Molecular simulation approaches to membrane proteins.
Dahkki: Stansfeld, P, et al.
Almmustuhtton: (2011)

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
Dahkki: Stansfeld, P, et al.
Almmustuhtton: (2011)

Multiscale simulations of lipid interactions with integral membrane proteins: aquaporins
Dahkki: Stansfeld, P, et al.
Almmustuhtton: (2011)

Coarse-grain simulations reveal movement of the synaptobrevin C-terminus in response to piconewton forces.
Dahkki: Lindau, M, et al.
Almmustuhtton: (2012)

Memprotmd: adding the grease to membrane protein structures
Dahkki: Stansfeld, P, et al.
Almmustuhtton: (2012)

Biomimetic design of a brush-like nanopore: simulation studies.
Dahkki: Pongprayoon, P, et al.
Almmustuhtton: (2012)

Water in transmembrane pores: Simulation studies.
Dahkki: Sansom, M, et al.
Almmustuhtton: (2001)

Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes
Dahkki: Domański, J, et al.
Almmustuhtton: (2020)

The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions
Dahkki: Newport, T, et al.
Almmustuhtton: (2018)

Computational studies of membrane proteins: from sequence to structure to simulation.
Dahkki: Stansfeld, P
Almmustuhtton: (2017)

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate.
Dahkki: Pongprayoon, P, et al.
Almmustuhtton: (2009)

Insights into membrane protein-lipid interactions from free energy calculations
Dahkki: Corey, R, et al.
Almmustuhtton: (2019)

Continuum vs. particle simulations of model nano-pores
Dahkki: Millar, C, et al.
Almmustuhtton: (2007)

The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores.
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2004)

A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor.
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2006)

Conformational Space and Dynamics of Sodium-Coupled Symporters
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2011)

The closed gate of the nicotinic receptor, identified by molecular dynamics free energy calculations
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2005)

The importance of surface character, geometry and flexibility in a hydrophobic gating mechanism for ion channels
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2004)

Liquid-vapor oscillations of water in hydrophobic nanopores.
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2003)

BioSimGrid: towards a worldwide repository for biomolecular simulations.
Dahkki: Tai, K, et al.
Almmustuhtton: (2004)

Simulations of the BM2 proton channel transmembrane domain from influenza virus B.
Dahkki: Rouse, S, et al.
Almmustuhtton: (2009)

Atomistic mechanism of transmembrane helix association.
Dahkki: Jan Domański, et al.
Almmustuhtton: (2020-06-01)

Interactions of the EphA2 kinase domain with PIPs in membranes: implications for receptor function
Dahkki: Chavent, M, et al.
Almmustuhtton: (2018)

Brownian simulation of charge transport in α-Haemolysin
Dahkki: Millar, C, et al.
Almmustuhtton: (2008)

Brownian simulation of charge transport in alpha-Haemolysin
Dahkki: Millar, C, et al.
Almmustuhtton: (2008)

The energetics of protein-lipid interactions as viewed by molecular simulations
Dahkki: Corey, RA, et al.
Almmustuhtton: (2019)

Energetics of protein interactions in the membrane via computer simulations
Dahkki: Domanski, J
Almmustuhtton: (2017)

A hydrophobic gating mechanism for nanopores
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2001)

Lipid loving ANTs: Molecular simulations of cardiolipin interactions and the organization of the adenine nucleotide translocase in model mitochondrial membranes
Dahkki: Sansom, M, et al.
Almmustuhtton: (2016)

Simulation-based prediction of phosphatidylinositol 4,5-bisphosphate binding to an ion channel.
Dahkki: Schmidt, MR, et al.
Almmustuhtton: (2013)

A BEST example of channel structure annotation by molecular simulation
Dahkki: Rao, S, et al.
Almmustuhtton: (2017)

Library adoption in public software repositories
Dahkki: Rachel Krohn, et al.
Almmustuhtton: (2019-05-01)

PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations.
Dahkki: Stansfeld, P, et al.
Almmustuhtton: (2009)

PIP2-binding site in Kir channels: definition by multiscale biomolecular simulations
Dahkki: Stansfeld, P, et al.
Almmustuhtton: (2009)

Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS
Dahkki: Jennifer Loschwitz, et al.
Almmustuhtton: (2021-04-01)

Features of the strawberry field repository formation
Dahkki: M. T. Upadyshev, et al.
Almmustuhtton: (2021-10-01)

Not ions alone: barriers to ion permeation in nanopores and channels.
Dahkki: Beckstein, O, et al.
Almmustuhtton: (2004)

Investigating the PIP2 Binding Site in Kir Channels Via Multi-Scale Biomolecular Simulations
Dahkki: Stansfeld, P, et al.
Almmustuhtton: (2010)