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The MARTINI Coarse-Grained Force Field: Extension to Proteins
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/bip.360221211openalex-snapshot
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
inferredcites →https://doi.org/10.1002/cphc.200600658openalex-snapshot
Comparison of Thermodynamic Properties of Coarse‐Grained and Atomic‐Level Simulation Models
inferredcites →https://doi.org/10.1002/jcc.10328openalex-snapshot
Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field
inferredcites →https://doi.org/10.1002/jcc.20090openalex-snapshot
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6
inferredcites →https://doi.org/10.1002/jcc.540130812openalex-snapshot
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
inferredcites →https://doi.org/10.1002/prot.21371openalex-snapshot
From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes
inferredcites →https://doi.org/10.1007/s00249-005-0005-yopenalex-snapshot
Multiscale modeling of lipids and lipid bilayers
inferredcites →https://doi.org/10.1016/0021-9991(77)90121-8openalex-snapshot
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
inferredcites →https://doi.org/10.1016/j.bbamem.2004.04.012openalex-snapshot
Computer simulations of membrane proteins
inferredcites →https://doi.org/10.1016/j.chemphyslip.2006.02.024openalex-snapshot
Modelling of proteins in membranes
inferredcites →https://doi.org/10.1016/j.cpc.2006.01.009openalex-snapshot
A systematic method to derive force fields for coarse-grained simulations of phospholipids
inferredcites →https://doi.org/10.1016/j.cplett.2005.07.075openalex-snapshot
A coarse grained model for the dynamics of flap opening in HIV-1 protease
inferredcites →https://doi.org/10.1016/j.jsb.2006.10.004openalex-snapshot
Coarse-grained molecular dynamics simulations of membrane proteins and peptides
inferredcites →https://doi.org/10.1016/j.physrep.2006.07.006openalex-snapshot
Mesoscopic models of biological membranes
inferredcites →https://doi.org/10.1016/j.physrep.2006.08.003openalex-snapshot
Biological and synthetic membranes: What can be learned from a coarse-grained description?
inferredcites →https://doi.org/10.1016/j.sbi.2007.03.004openalex-snapshot
Multiscale modeling of biomolecular systems: in serial and in parallel
inferredcites →https://doi.org/10.1016/s0014-5793(04)00271-6openalex-snapshot
Computer simulation of the KvAP voltage‐gated potassium channel: steered molecular dynamics of the voltage sensor
inferredcites →https://doi.org/10.1016/s0022-2836(02)00627-7openalex-snapshot
Exploring Global Distortions of Biological Macromolecules and Assemblies from Low-resolution Structural Information and Elastic Network Theory
inferredcites →https://doi.org/10.1016/s1359-0278(97)00024-2openalex-snapshot
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
inferredcites →https://doi.org/10.1021/bi00405a042openalex-snapshot
Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
inferredcites →https://doi.org/10.1021/bi00507a030openalex-snapshot
Affinities of amino acid side chains for solvent water
inferredcites →https://doi.org/10.1021/bi980233ropenalex-snapshot
Influence of Lipid/Peptide Hydrophobic Mismatch on the Thickness of Diacylphosphatidylcholine Bilayers. A 2H NMR and ESR Study Using Designed Transmembrane α-Helical Peptides and Gramicidin A
inferredcites →https://doi.org/10.1021/ja00214a001openalex-snapshot
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
inferredcites →https://doi.org/10.1021/ja0352092openalex-snapshot
Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles
inferredcites →https://doi.org/10.1021/ja037010vopenalex-snapshot
Association Lifetimes of Hydrophobic Amino Acid Pairs Measured Directly from Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/ja039159copenalex-snapshot
Molecular Simulations Suggest Protein Salt Bridges Are Uniquely Suited to Life at High Temperatures
inferredcites →https://doi.org/10.1021/ja0569104openalex-snapshot
Insertion and Assembly of Membrane Proteins via Simulation
inferredcites →https://doi.org/10.1021/ja0706246openalex-snapshot
G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers
inferredcites →https://doi.org/10.1021/ja073784qopenalex-snapshot
On the Orientation of a Designed Transmembrane Peptide: Toward the Right Tilt Angle?
inferredcites →https://doi.org/10.1021/ja970503dopenalex-snapshot
Experimental and Theoretical Approach to Hydrogen-Bonded Diastereomeric Interactions in a Model Complex
inferredcites →https://doi.org/10.1021/jp010238popenalex-snapshot
A Coarse Grain Model for Phospholipid Simulations
inferredcites →https://doi.org/10.1021/jp036508gopenalex-snapshot
Coarse Grained Model for Semiquantitative Lipid Simulations
inferredcites →https://doi.org/10.1021/jp044629qopenalex-snapshot
A Multiscale Coarse-Graining Method for Biomolecular Systems
inferredcites →https://doi.org/10.1021/jp0550816openalex-snapshot
Coarse Grained Protein−Lipid Model with Application to Lipoprotein Particles
inferredcites →https://doi.org/10.1021/jp062012yopenalex-snapshot
Coarse-Grained Transmembrane Proteins: Hydrophobic Matching, Aggregation, and Their Effect on Fusion
inferredcites →https://doi.org/10.1021/jp062700hopenalex-snapshot
Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel
inferredcites →https://doi.org/10.1021/jp071097fopenalex-snapshot
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
inferredcites →https://doi.org/10.1021/jp709675eopenalex-snapshot
Gating Motions in Voltage-Gated Potassium Channels Revealed by Coarse-Grained Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/la0492759openalex-snapshot
Simulation of Domain Formation in DLPC−DSPC Mixed Bilayers
inferredcites →https://doi.org/10.1021/ma00145a039openalex-snapshot
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
inferredcites →https://doi.org/10.1038/253694a0openalex-snapshot
Computer simulation of protein folding
inferredcites →https://doi.org/10.1038/nsb1096-842openalex-snapshot
Experimentally determined hydrophobicity scale for proteins at membrane interfaces
inferredcites →https://doi.org/10.1063/1.1587119openalex-snapshot
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
inferredcites →https://doi.org/10.1063/1.1861455openalex-snapshot
Mesoscale model of polymer melt structure: Self-consistent mapping of molecular correlations to coarse-grained potentials
inferredcites →https://doi.org/10.1063/1.2187488openalex-snapshot
Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems
inferredcites →https://doi.org/10.1063/1.2714540openalex-snapshot
A macromolecule in a solvent: Adaptive resolution molecular dynamics simulation
inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot
Molecular dynamics with coupling to an external bath
inferredcites →https://doi.org/10.1063/1.456500openalex-snapshot
Intrachain loops in polymers: Effects of excluded volume
inferredcites →https://doi.org/10.1073/pnas.0408885102openalex-snapshot
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
inferredcites →https://doi.org/10.1073/pnas.0409471102openalex-snapshot
Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
inferredcites →https://doi.org/10.1073/pnas.0507618102openalex-snapshot
Interface connections of a transmembrane voltage sensor
inferredcites →https://doi.org/10.1073/pnas.0606822104openalex-snapshot
Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations
inferredcites →https://doi.org/10.1073/pnas.75.2.559openalex-snapshot
Respective roles of short- and long-range interactions in protein folding.
inferredcites →https://doi.org/10.1073/pnas.97.7.3189openalex-snapshot
Electrospray ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of transmembrane peptides in lipid bilayers
inferredcites →https://doi.org/10.1074/jbc.m502810200openalex-snapshot
Self-association of Transmembrane α-Helices in Model Membranes
inferredcites →https://doi.org/10.1085/jgp.200709745openalex-snapshot
Partitioning of Amino Acid Side Chains into Lipid Bilayers: Results from Computer Simulations and Comparison to Experiment
inferredcites →https://doi.org/10.1088/0953-8984/18/28/s06openalex-snapshot
The computational route from bilayer membranes to vesicle fusion
inferredcites →https://doi.org/10.1088/0953-8984/18/28/s07openalex-snapshot
Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins
inferredcites →https://doi.org/10.1103/physrevlett.95.218102openalex-snapshot
Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site
inferredcites →https://doi.org/10.1103/physrevlett.96.028105openalex-snapshot
Resolution Exchange Simulation
inferredcites →https://doi.org/10.1529/biophysj.103.035402openalex-snapshot
Tilt Angles of Transmembrane Model Peptides in Oriented and Non-Oriented Lipid Bilayers as Determined by 2H Solid-State NMR
inferredcites →https://doi.org/10.1529/biophysj.104.048710openalex-snapshot
Molecular View of Hexagonal Phase Formation in Phospholipid Membranes
inferredcites →https://doi.org/10.1529/biophysj.104.050849openalex-snapshot
Simulation Studies of Protein-Induced Bilayer Deformations, and Lipid-Induced Protein Tilting, on a Mesoscopic Model for Lipid Bilayers with Embedded Proteins
inferredcites →https://doi.org/10.1529/biophysj.105.068080openalex-snapshot
Many-Body Effect of Antimicrobial Peptides: On the Correlation Between Lipid’s Spontaneous Curvature and Pore Formation
inferredcites →https://doi.org/10.1529/biophysj.105.073395openalex-snapshot
Molecular Dynamics Simulations of Model Trans-Membrane Peptides in Lipid Bilayers: A Systematic Investigation of Hydrophobic Mismatch
inferredcites →https://doi.org/10.1529/biophysj.106.082776openalex-snapshot
Curvature and Hydrophobic Forces Drive Oligomerization and Modulate Activity of Rhodopsin in Membranes
inferredcites →https://doi.org/10.1529/biophysj.106.093013openalex-snapshot
Self-Assembling of Peptide/Membrane Complexes by Atomistic Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1529/biophysj.106.093443openalex-snapshot
Coarse-Grained Molecular Dynamics Simulations of a Rotating Bacterial Flagellum
inferredcites →https://doi.org/10.1529/biophysj.107.112805openalex-snapshot
Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations
inferredcites →https://doi.org/10.1529/biophysj.107.113043openalex-snapshot
The Dynamic Orientation of Membrane-Bound Peptides: Bridging Simulations and Experiments
inferredcites →https://doi.org/10.1529/biophysj.107.115857openalex-snapshot
Structure of Spheroidal HDL Particles Revealed by Combined Atomistic and Coarse-Grained Simulations
inferredcites →https://doi.org/10.1529/biophysj.107.119966openalex-snapshot
Mechanosensitive Membrane Channels in Action
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.2139/ssrn.4848482openalex-extracted
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inferred← citeshttps://doi.org/10.1002/1873-3468.13186openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/1873-3468.13277openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/1873-3468.14490openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/3527600434.eap665openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118482568.ch15openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118523063.ch14openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118523063.ch9openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118998861.ch9openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781394316632.ch17openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527830503.ch8openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527834044.ch43openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adfm.201400956openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adfm.202532052openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adhm.201200400openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adhm.202505685openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adma.201403361openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adma.202008635openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adma.202204272openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adma.202311467openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adts.201800105openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adts.202200628openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/advs.201800471openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/advs.202301544openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/advs.202511483openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/advs.202513911openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/aic.16847openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/aidi.202500163openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.202112232openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.202303755openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.6392855openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.202112232openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.202303755openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/bip.21474openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cbic.201100020openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cbic.201200715openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cbic.202200723openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cite.201400095openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cjce.23761openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.200900216openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.202200509openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ddr.21472openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ijch.201400006openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ijch.201400035openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ijch.201400188openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21223openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21415openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21871openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21915openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21927openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21990openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.22883openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.22915openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23693openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23929openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24391openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24404openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24517openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24660openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24694openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24845openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24895openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.25747openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.25773openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.26070openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.26110openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.26131openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.26214openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.27003openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jmr.2412openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/marc.201300360openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/marc.202100683openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/masy.202100443openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201100005openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201100010openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201100011openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201100022openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201200078openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201300101openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201500023openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mats.201500041openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pep2.24120openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.3421openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4732openalex-snapshot
Human aromatic amino acid decarboxylase is an asymmetric and flexible enzyme: Implication in aromatic amino acid decarboxylase deficiency
inferred← citeshttps://doi.org/10.1002/pro.5172openalex-snapshot
A coarse‐grained model for disordered and multi‐domain proteins
inferred← citeshttps://doi.org/10.1002/pro.70013openalex-snapshot
An in silico framework to visualize how cancer‐associated mutations influence structural plasticity of the chemokine receptor CCR3
inferred← citeshttps://doi.org/10.1002/pro.70480openalex-snapshot
Compartment‐guided assembly of large‐scale molecular models with Bentopy
inferred← citeshttps://doi.org/10.1002/pro.70793openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.22645openalex-snapshot
PRIMO/PRIMONA: A coarse‐grained model for proteins and nucleic acids that preserves near‐atomistic accuracy
inferred← citeshttps://doi.org/10.1002/prot.23044openalex-snapshot
Leukocyte integrin αLβ2 transmembrane association dynamics revealed by coarse‐grained molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/prot.24070openalex-snapshot
The role of domain: Domain interactions versus domain: Water interactions in the coarse‐grained simulations of the E1P to E2P transitions in Ca‐ATPase (SERCA)
inferred← citeshttps://doi.org/10.1002/prot.24108openalex-snapshot
Coarse grain lipid–protein molecular interactions and diffusion with MsbA flippase
inferred← citeshttps://doi.org/10.1002/prot.24164openalex-snapshot
Combining coarse‐grained nonbonded and atomistic bonded interactions for protein modeling
inferred← citeshttps://doi.org/10.1002/prot.24263openalex-snapshot
Thermodynamic analysis of structural transitions during GNNQQNY aggregation
inferred← citeshttps://doi.org/10.1002/prot.24407openalex-snapshot
Delaunay‐based nonlocal interactions are sufficient and accurate in protein fold recognition
inferred← citeshttps://doi.org/10.1002/prot.24454openalex-snapshot
A global machine learning based scoring function for protein structure prediction
inferred← citeshttps://doi.org/10.1002/prot.24609openalex-snapshot
De novoinference of protein function from coarse-grained dynamics
inferred← citeshttps://doi.org/10.1002/prot.24703openalex-snapshot
Computational modeling of membrane proteins
inferred← citeshttps://doi.org/10.1002/prot.24845openalex-snapshot
A multiscale approach to simulating the conformational properties of unbound multi‐ C 2 H 2 zinc finger proteins
inferred← citeshttps://doi.org/10.1002/prot.24934openalex-snapshot
Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization
inferred← citeshttps://doi.org/10.1002/prot.24958openalex-snapshot
Refining the treatment of membrane proteins by coarse‐grained models
inferred← citeshttps://doi.org/10.1002/prot.25156openalex-snapshot
M olecular aspects of the interaction between M ason— P fizer monkey virus matrix protein and artificial phospholipid membrane
inferred← citeshttps://doi.org/10.1002/prot.25273openalex-snapshot
S elf‐assembling study of sarcolipin and its mutants in multiple molecular dynamic simulations
inferred← citeshttps://doi.org/10.1002/prot.25297openalex-snapshot
Insights into the transmembrane helix associations of kit ligand by molecular dynamics simulation and TOXCAT
inferred← citeshttps://doi.org/10.1002/prot.25498openalex-snapshot
The dimerization of PSGL‐1 is driven by the transmembrane domain via a leucine zipper motif
inferred← citeshttps://doi.org/10.1002/prot.25854openalex-snapshot
Computational simulations of TNF receptor oligomerization on plasma membrane
inferred← citeshttps://doi.org/10.1002/prot.25869openalex-snapshot
An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45
inferred← citeshttps://doi.org/10.1002/prot.26037openalex-snapshot
Using normal mode analysis on protein structural models. How far can we go on our predictions?
inferred← citeshttps://doi.org/10.1002/prot.26352openalex-snapshot
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation
inferred← citeshttps://doi.org/10.1002/prot.26401openalex-snapshot
The effect of lipid composition on the dynamics of tau fibrils
inferred← citeshttps://doi.org/10.1002/qub2.20openalex-snapshot
Toward atomistic models of intact severe acute respiratory syndrome coronavirus 2 via Martini coarse‐grained molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/qub2.70024openalex-snapshot
Advances and challenges in multiscale biomolecular simulations: artificial intelligence‐driven paradigm shift
inferred← citeshttps://doi.org/10.1002/smll.201401943openalex-snapshot
Theoretical and Computational Investigations of Nanoparticle–Biomembrane Interactions in Cellular Delivery
inferred← citeshttps://doi.org/10.1002/smll.201603708openalex-snapshot
Lipid Flip-Flop and Pore Nucleation on Zwitterionic Bilayers are Asymmetric under Ionic Imbalance
inferred← citeshttps://doi.org/10.1002/smll.202005743openalex-snapshot
3D Printing of Supramolecular Polymer Hydrogels with Hierarchical Structure
inferred← citeshttps://doi.org/10.1002/smll.202200921openalex-snapshot
Nanopore Sensing Technique for Studying the Hofmeister Effect
inferred← citeshttps://doi.org/10.1002/smll.202403913openalex-snapshot
Hydrodynamics and Aggregation of Nanoparticles with Protein Corona: Effects of Protein Concentration and Ionic Strength
inferred← citeshttps://doi.org/10.1002/smll.202513399openalex-snapshot
Mechanistic Insight Into Ionizable Cationic Lipid‐Mediated Endosomal Escape via Transient Lipid Complexes
inferred← citeshttps://doi.org/10.1002/solr.202200172openalex-snapshot
A Theoretical Perspective on the Thermodynamic Stability of Polymer Blends for Solar Cells: From Experiments to Predictive Modeling
inferred← citeshttps://doi.org/10.1002/syst.202200040openalex-snapshot
Designed Complex Peptide‐Based Adaptive Systems: A Bottom‐Up Approach
inferred← citeshttps://doi.org/10.1002/wcms.1169openalex-snapshot
The power of coarse graining in biomolecular simulations
inferred← citeshttps://doi.org/10.1002/wcms.1277openalex-snapshot
Organic–inorganic interface simulation for new material discoveries
inferred← citeshttps://doi.org/10.1002/wcms.1306openalex-snapshot
Molecular ‘time‐machines’ to unravel key biological events for drug design
inferred← citeshttps://doi.org/10.1002/wcms.1620openalex-snapshot
Two decades of Martini: Better beads, broader scope
inferred← citeshttps://doi.org/10.1007/128_2010_122openalex-snapshot
Coarse-Grained Modeling for Macromolecular Chemistry
inferred← citeshttps://doi.org/10.1007/12_2013_258openalex-snapshot
Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications
inferred← citeshttps://doi.org/10.1007/978-1-0716-0892-0_18openalex-snapshot
Protocol for Simulations of PEGylated Proteins with Martini 3
inferred← citeshttps://doi.org/10.1007/978-1-0716-0928-6_6openalex-snapshot
Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes
inferred← citeshttps://doi.org/10.1007/978-1-0716-1394-8_14openalex-snapshot
Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide
inferred← citeshttps://doi.org/10.1007/978-1-0716-1468-6_8openalex-snapshot
Identification and Characterization of Specific Protein–Lipid Interactions Using Molecular Simulation
inferred← citeshttps://doi.org/10.1007/978-1-0716-1546-1_16openalex-snapshot
Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations
inferred← citeshttps://doi.org/10.1007/978-1-0716-1546-1_4openalex-snapshot
Computational Models for the Study of Protein Aggregation
inferred← citeshttps://doi.org/10.1007/978-1-0716-1716-8_23openalex-snapshot
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
inferred← citeshttps://doi.org/10.1007/978-1-0716-1855-4_7openalex-snapshot
Coarse-Grain Simulations of Membrane-Adsorbed Helical Peptides
inferred← citeshttps://doi.org/10.1007/978-1-0716-3985-6_12openalex-snapshot
Challenges of Protein-Protein Docking of the Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-1-0716-5054-7_1openalex-snapshot
Characterization of Membrane Binding and Protein–Lipid Interactions at the Atomic Level with an Accelerated HMMM Model
inferred← citeshttps://doi.org/10.1007/978-1-0716-5054-7_32openalex-snapshot
Multiscale Simulation Approaches to Probe Lipid Interactions of G Protein-Coupled Receptors
inferred← citeshttps://doi.org/10.1007/978-1-4419-6889-0_3openalex-snapshot
Coarse-Grained Models of Proteins: Theory and Applications
inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_4openalex-snapshot
Lipid Membranes for Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_7openalex-snapshot
Coarse-Grained Force Fields for Molecular Simulations
inferred← citeshttps://doi.org/10.1007/978-1-4939-1752-5_20openalex-snapshot
Cholesterol Behavior in Asymmetric Lipid Bilayers: Insights from Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1007/978-1-4939-2285-7_9openalex-snapshot
In Silico Design of Antimicrobial Peptides
inferred← citeshttps://doi.org/10.1007/978-1-4939-3179-8_40openalex-snapshot
MD Simulations of P-Type ATPases in a Lipid Bilayer System
inferred← citeshttps://doi.org/10.1007/978-1-4939-6940-1_6openalex-snapshot
Method for Developing Optical Sensors Using a Synthetic Dye-Fluorescent Protein FRET Pair and Computational Modeling and Assessment
inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_2openalex-snapshot
Recent Advances in Computational Approaches for Designing Potential Anti-Alzheimer’s Agents
inferred← citeshttps://doi.org/10.1007/978-1-4939-9512-7_1openalex-snapshot
Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-4939-9516-5_21openalex-snapshot
Molecular-Level “Observations” of the Behavior of Gold Nanoparticles in Aqueous Solution and Interacting with a Lipid Bilayer Membrane
inferred← citeshttps://doi.org/10.1007/978-1-4939-9608-7_5openalex-snapshot
A Practical View of the Martini Force Field
inferred← citeshttps://doi.org/10.1007/978-1-60761-314-5_1openalex-snapshot
Molecular Theory Applied to Lipid Bilayers and Lipid–Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-60761-325-1_18openalex-snapshot
Visualization of Complex Processes in Lipid Systems Using Computer Simulations and Molecular Graphics
inferred← citeshttps://doi.org/10.1007/978-1-60761-762-4_21openalex-snapshot
Molecular Dynamics of Membrane Peptides and Proteins: Principles and Comparison to Experimental Data
inferred← citeshttps://doi.org/10.1007/978-1-60761-762-4_22openalex-snapshot
Membrane Protein Dynamics from Femtoseconds to Seconds
inferred← citeshttps://doi.org/10.1007/978-1-62703-017-5_19openalex-snapshot
Systematic Methods for Structurally Consistent Coarse-Grained Models
inferred← citeshttps://doi.org/10.1007/978-1-62703-017-5_20openalex-snapshot
The Martini Coarse-Grained Force Field
inferred← citeshttps://doi.org/10.1007/978-1-62703-017-5_22openalex-snapshot
Coarse-Grained Models for Protein Folding and Aggregation
inferred← citeshttps://doi.org/10.1007/978-1-62703-017-5_25openalex-snapshot
Multiscale Molecular Dynamics Simulations of Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-1-62703-275-9_19openalex-snapshot
The Simulation Approach to Lipid–Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-62703-487-6_6openalex-snapshot
Molecular Dynamics Simulations of Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-1-62703-658-0_7openalex-snapshot
Balancing Bond, Nonbond, and Gō-Like Terms in Coarse Grain Simulations of Conformational Dynamics
inferred← citeshttps://doi.org/10.1007/978-3-030-11596-8_5openalex-snapshot
Molecular Dynamics Studies of Nanoparticle Transport Through Model Lipid Membranes
inferred← citeshttps://doi.org/10.1007/978-3-030-36260-7_10openalex-snapshot
Molecular Dynamics Simulations in Drug Discovery and Drug Delivery
inferred← citeshttps://doi.org/10.1007/978-3-030-60124-9_9openalex-snapshot
Nanomaterials Interaction with Cell Membranes: Computer Simulation Studies
inferred← citeshttps://doi.org/10.1007/978-3-030-62226-8_2openalex-snapshot
Review: Simulation Models for Materials and Biomolecules
inferred← citeshttps://doi.org/10.1007/978-3-030-81576-9_5openalex-snapshot
Molecular Modeling for Reliability Issues
inferred← citeshttps://doi.org/10.1007/978-3-030-83244-5_2openalex-snapshot
Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
inferred← citeshttps://doi.org/10.1007/978-3-031-29360-3_9openalex-snapshot
In Silico Prediction of Peptide Self-assembly into Nanostructures
inferred← citeshttps://doi.org/10.1007/978-3-031-34839-6_7openalex-snapshot
Coarse-Grain Modelling Strategies
inferred← citeshttps://doi.org/10.1007/978-3-031-46870-4_4openalex-snapshot
Molecular Dynamics Simulations of the Structure of Lipid-Based Nanomaterials
inferred← citeshttps://doi.org/10.1007/978-3-031-73730-5_1openalex-snapshot
Introduction to Atomistic Modeling and Simulation of Biomolecular Systems
inferred← citeshttps://doi.org/10.1007/978-3-031-98022-0_9openalex-snapshot
Harnessing Artificial Intelligence to Revolutionise Molecular Modelling and Simulations
inferred← citeshttps://doi.org/10.1007/978-3-319-01008-3_15openalex-snapshot
Modeling of Lipid Membranes and Lipoproteins
inferred← citeshttps://doi.org/10.1007/978-3-319-02970-2_13openalex-snapshot
Molecular Dynamics Simulation of Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-3-319-02970-2_18openalex-snapshot
Chemosensorial G-proteins-Coupled Receptors: A Perspective from Computational Methods
inferred← citeshttps://doi.org/10.1007/978-3-319-02970-2_7openalex-snapshot
Coarse-Grained Models of the Proteins Backbone Conformational Dynamics
inferred← citeshttps://doi.org/10.1007/978-3-319-11280-0_16openalex-snapshot
Role of Lipid-Mediated Effects in β2-Adrenergic Receptor Dimerization
inferred← citeshttps://doi.org/10.1007/978-3-319-19454-7_109-1openalex-snapshot
Atomistic Simulation of Sol–Gel-Derived Hybrid Materials
inferred← citeshttps://doi.org/10.1007/978-3-319-20040-8_1openalex-snapshot
Amyloid and Amyloid Fibrils
inferred← citeshttps://doi.org/10.1007/978-3-319-20040-8_6openalex-snapshot
Coarse Grained Study of Amyloid Protofibril Aggregation
inferred← citeshttps://doi.org/10.1007/978-3-319-20164-1_2openalex-snapshot
Structure and Dynamics of Intrinsically Disordered Proteins
inferred← citeshttps://doi.org/10.1007/978-3-319-22345-2_6openalex-snapshot
Morphogenic Peptides in Regeneration of Load Bearing Tissues
inferred← citeshttps://doi.org/10.1007/978-3-319-22977-5_46-1openalex-snapshot
Molecular Dynamics-Decorated Finite Element Method (MDeFEM): Application to the Gating Mechanism of Mechanosensitive Channels
inferred← citeshttps://doi.org/10.1007/978-3-319-32101-1_109openalex-snapshot
Atomistic Simulation of Sol‐Gel-Derived Hybrid Materials
inferred← citeshttps://doi.org/10.1007/978-3-319-43676-0_52-1openalex-snapshot
Modeling Lipid Membranes
inferred← citeshttps://doi.org/10.1007/978-3-319-50430-8_52openalex-snapshot
Modeling Lipid Membranes
inferred← citeshttps://doi.org/10.1007/978-3-319-55539-3_8openalex-snapshot
Lipids in Regulation of the Mitochondrial Outer Membrane Permeability, Bioenergetics, and Metabolism
inferred← citeshttps://doi.org/10.1007/978-3-319-56895-9_2openalex-snapshot
Role of Bioinformatics in the Study of Ionic Channels
inferred← citeshttps://doi.org/10.1007/978-3-319-58729-5_46openalex-snapshot
Molecular Dynamics-Decorated Finite Element Method (MDeFEM): Application to the Gating Mechanism of Mechanosensitive Channels
inferred← citeshttps://doi.org/10.1007/978-3-319-95843-9_12openalex-snapshot
Modeling of Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-3-319-96842-1_9openalex-snapshot
Intracellular Membrane Trafficking: Modeling Local Movements in Cells
inferred← citeshttps://doi.org/10.1007/978-3-319-97277-0_21openalex-snapshot
Molecular Dynamics Study of the Solution Behaviour of Antimicrobial Peptide Indolicidin
inferred← citeshttps://doi.org/10.1007/978-3-642-28554-7_12openalex-snapshot
Modeling of Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-3-7091-1574-9_2openalex-snapshot
Multi-scale modeling of biomaterials and tissues
inferred← citeshttps://doi.org/10.1007/978-3-7091-1574-9_4openalex-snapshot
Multiscale modeling of diffusion phenomena in polymers
inferred← citeshttps://doi.org/10.1007/978-94-007-1611-7_6openalex-snapshot
Computational Approaches and Simulation
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