Research graph
References from In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come?. Local targets link to admitted publications; unresolved targets remain external evidence.
The Gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields
10.1002/jcc.25823 · 2019 · External reference
10.1016/j.bbalip.2016.10.006
10.1016/j.bbalip.2016.10.006 · External reference
Role of O-antigen in response to mechanical stress of the E. coli outer membrane: insights from coarse-grained MD simulations
10.1021/acs.jpcb.8b12168 · 2019 · External reference
10.1016/j.bbamem.2019.07.013
10.1016/j.bbamem.2019.07.013 · External reference
Antibiotic hybrids: The next generation of agents and adjuvants against gram-negative pathogens?
10.1128/cmr.00077-17 · 2018 · External reference
10.1021/cb4003199
10.1021/cb4003199 · External reference
Modeling and simulation of bacterial outer membranes with lipopolysaccharides and enterobacterial common antigen
10.1021/acs.jpcb.0c03353 · 2020 · External reference
Unresolved reference
2021 · External reference
Function and biogenesis of Lipopolysaccharides
10.1128/ecosalplus.esp-0001-2018 · 2018 · External reference
10.1016/s0168-1656(99)00185-6
10.1016/s0168-1656(99)00185-6 · External reference
10.1016/j.ijmm.2016.03.001
10.1016/j.ijmm.2016.03.001 · External reference
Ionic environment affects bacterial lipopolysaccharide packing and function
10.1021/acs.langmuir.9b03162 · 2020 · External reference
10.1002/prot.24223
10.1002/prot.24223 · External reference
10.1016/j.anres.2018.08.002
10.1016/j.anres.2018.08.002 · External reference
10.1016/j.str.2018.04.007
10.1016/j.str.2018.04.007 · External reference
Outer membrane permeability barrier in Escherichia coli mutants that are defective in the late acyltransferases of lipid A biosynthesis
10.1128/aac.43.6.1459 · 1999 · External reference
Lipopolysaccharide Simulations Are Sensitive to Phosphate Charge and Ion Parameterization
10.1021/acs.jctc.9b00868 · 2020 · External reference
Modeling of specific Lipopolysaccharide binding sites on a Gram-negative porin
10.1021/acs.jpcb.9b03669 · 2019 · External reference
10.1016/j.bbamem.2006.05.017
10.1016/j.bbamem.2006.05.017 · External reference
The stories tryptophans tell: exploring protein dynamics of heptosyltransferase I from Escherichia coli
10.1021/acs.biochem.6b00850 · 2017 · External reference
10.1016/j.tim.2004.02.009
10.1016/j.tim.2004.02.009 · External reference
10.1002/cmdc.201800505
10.1002/cmdc.201800505 · External reference
Progress in molecular dynamics simulations of Gram-negative bacterial cell envelopes
10.1021/acs.jpclett.7b00473 · 2017 · External reference
10.1016/j.jmgm.2020.107625
10.1016/j.jmgm.2020.107625 · External reference
10.1038/nm.3640
10.1038/nm.3640 · External reference
Predicting binding free energies: Frontiers and benchmarks
10.1146/annurev-biophys-070816-033654 · 2017 · External reference
Molecular simulations in drug delivery: Opportunities and challenges
10.1002/wcms.1358 · 2018 · External reference
Molecular dynamics simulations: concept, methods and applications
2020 · External reference
Unresolved reference
2016 · External reference
Fighting against bacterial lipopolysaccharide-caused infections through molecular dynamics simulations: A review
10.1021/acs.jcim.1c00613 · 2021 · External reference
10.1021/ja991374z
10.1021/ja991374z · External reference
Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa
10.1016/s0006-3495(01)75761-x · 2001 · External reference
Assessing Barriers for Antimicrobial Penetration in Complex Asymmetric Bacterial Membranes: A Case Study with Thymol
10.1021/acs.langmuir.0c01124 · 2020 · External reference
Homology modeling, docking and structure-based virtual screening for new inhibitor identification of Klebsiella pneumoniae heptosyltransferase-III
10.1080/07391102.2019.1624296 · 2020 · External reference
10.1002/(sici)1097-0282(199703)41:3<251::aid-bip2>3.0.co;2-r
10.1002/(sici)1097-0282(199703)41:3<251::aid-bip2>3.0.co;2-r · External reference
Novel carboxylate-based glycolipids: TLR4 antagonism, MD-2 binding and self-assembly properties
10.1038/s41598-018-37421-w · 2019 · External reference
Molecular modeling of neurological membrane proteins − from binding sites to synapses
10.1016/j.neulet.2018.05.034 · 2019 · External reference
10.1016/j.neuron.2018.08.011
10.1016/j.neuron.2018.08.011 · External reference
10.1038/nsb0902-646
10.1038/nsb0902-646 · External reference
10.1021/acs.jcim.7b00271
10.1021/acs.jcim.7b00271 · External reference
10.1016/j.bbamem.2017.07.010
10.1016/j.bbamem.2017.07.010 · External reference
10.1371/journal.pcbi.1007228
10.1371/journal.pcbi.1007228 · External reference
Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations
10.1016/j.jconrel.2021.03.005 · 2021 · External reference
10.1146/annurev-biophys-042910-155245
10.1146/annurev-biophys-042910-155245 · External reference
The impact of molecular dynamics on drug design: Applications for the characterization of ligand-macromolecule complexes
10.1016/j.drudis.2015.01.003 · 2015 · External reference
10.1007/s12551-015-0189-z
10.1007/s12551-015-0189-z · External reference
Recent advances in transferable coarse-grained modeling of proteins
10.1016/bs.apcsb.2014.06.005 · 2014 · External reference
10.1063/1674-0068/cjcp1905091
10.1063/1674-0068/cjcp1905091 · External reference
Reaction coordinates in complex systems-a perspective
10.1140/epjb/s10051-021-00233-5 · 2021 · External reference
Data-driven computation of molecular reaction coordinates
10.1063/1.5035183 · 2018 · External reference
Identification of simple reaction coordinates from complex dynamics
10.1063/1.4974306 · 2017 · External reference
10.1002/wcms.66
10.1002/wcms.66 · External reference
Reaction Coordinates and Mechanistic Hypothesis Tests
10.1146/annurev-physchem-040215-112215 · 2016 · External reference
10.1145/1364782.1364802
10.1145/1364782.1364802 · External reference
10.1109/sc.2014.9
10.1109/sc.2014.9 · External reference
10.1007/s12551-011-0063-6 · Admitted local publication
Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method
10.1002/jcc.10193 · 2003 · External reference
10.1007/978-0-387-09766-4
10.1007/978-0-387-09766-4 · 2011 · External reference
Free energy, enthalpy and entropy from implicit solvent end-point simulations
10.3389/fmolb.2018.00011 · 2018 · External reference
Solvated Interaction Energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space
10.1021/ci600406v · 2007 · External reference
On Calculating Free Energy Differences Using Ensembles of Transition Paths
10.3389/fmolb.2020.00106 · 2020 · External reference
Computation of Free Energy
10.1002/1522-2675(200210)85:10<3113::aid-hlca3113>3.0.co;2-0 · 2002 · External reference
Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?
10.1021/acs.jctc.8b01142 · 2019 · External reference
Exploring Conformational Transitions and Free-Energy Profiles of Proton-Coupled Oligopeptide Transporters
10.1021/acs.jctc.9b00524 · 2019 · External reference
10.1126/science.8153625
10.1126/science.8153625 · External reference
Salmonella membrane structural remodeling increases resistance to antimicrobial peptide LL-37
10.1021/acsinfecdis.9b00066 · 2019 · External reference
10.1016/j.bpj.2018.02.006
10.1016/j.bpj.2018.02.006 · External reference
10.1128/jb.00973-07
10.1128/jb.00973-07 · External reference
Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability
10.1016/j.bpj.2016.01.002 · 2016 · External reference
10.1016/j.bpj.2014.04.016
10.1016/j.bpj.2014.04.016 · External reference
10.1021/jp506633n
10.1021/jp506633n · External reference
10.1021/acs.jctc.8b01059
10.1021/acs.jctc.8b01059 · External reference
10.1073/pnas.1602382113
10.1073/pnas.1602382113 · External reference
10.3390/ijms20153774
10.3390/ijms20153774 · External reference
10.1007/978-94-007-0711-5_7
10.1007/978-94-007-0711-5_7 · 2012 · External reference
10.1371/journal.pone.0183889
10.1371/journal.pone.0183889 · External reference
10.3390/ijms19123899
10.3390/ijms19123899 · External reference
10.1021/ct9002114
10.1021/ct9002114 · External reference
10.1021/acs.jpclett.7b02432
10.1021/acs.jpclett.7b02432 · External reference
Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers
10.1021/acs.jctc.0c00539 · 2020 · External reference
10.1021/acs.jcim.8b00261
10.1021/acs.jcim.8b00261 · External reference
Ligand Pathways in Nuclear Receptors
10.1021/acs.jcim.9b00360 · 2019 · External reference
An improved strategy for generating forces in steered molecular dynamics: The mechanical unfolding of titin, e2lip3 and ubiquitin
10.1371/journal.pone.0013068 · 2010 · External reference
10.1016/j.bbamem.2015.12.032
10.1016/j.bbamem.2015.12.032 · External reference
Ligand binding free energy and kinetics calculation in 2020
10.1002/wcms.1455 · 2020 · External reference
10.1002/cphc.202000219
10.1002/cphc.202000219 · External reference
Efficient determination of free energy landscapes in multiple dimensions from biased Umbrella sampling simulations using linear regression
10.1021/ct501130r · 2015 · External reference
The adsorption of human defensin 5 on bacterial membranes: simulation studies
10.1007/s00894-018-3812-7 · 2018 · External reference
The penetration of human defensin 5 (HD5) through bacterial outer membrane: simulation studies
10.1007/s00894-021-04915-w · 2021 · External reference
10.3390/ijms222212401
10.3390/ijms222212401 · External reference
Molecular dynamics simulations of the host defense peptide temporin L and Its Q3K Derivative: An atomic level view from aggregation in water to bilayer perturbation
10.3390/molecules22071235 · 2017 · External reference
The Tug of War between Al3+ and Na+ for Order-Disorder Transitions in Lipid-A Membranes
10.1039/d1cp02173g · 2021 · External reference
Peptide VSAK maintains tissue glucose uptake and attenuates pro-inflammatory responses caused by LPS in an experimental model of the systemic inflammatory response syndrome: a PET study
10.1038/s41598-021-94224-2 · 2021 · External reference
Influences of Vibrio cholerae Lipid A Types on LPS Bilayer Properties
10.1021/acs.jpcb.0c09144 · 2021 · External reference
10.1016/j.csbj.2021.06.051
10.1016/j.csbj.2021.06.051 · External reference
10.1016/j.cell.2019.12.006
10.1016/j.cell.2019.12.006 · External reference
Molecular characterization of the outer membrane of Pseudomonas aeruginosa
10.1016/j.bbamem.2019.183151 · 2020 · External reference
Structural insights into the membrane receptor ShuA in DDM micelles and in a model of gram-negative bacteria outer membrane as seen by SAXS and MD simulations
10.1016/j.bbamem.2020.183504 · 2021 · External reference
10.1021/acs.jpcb.8b07109
10.1021/acs.jpcb.8b07109 · External reference
Refinement of OprH-LPS interactions by molecular simulations
10.1016/j.bpj.2016.12.006 · 2017 · External reference
Computational Investigation of Bisphosphate Inhibitors of 3-Deoxy-d-manno-octulosonate 8-phosphate Synthase
10.3390/molecules24132370 · 2019 · External reference
10.1016/j.mib.2013.09.007
10.1016/j.mib.2013.09.007 · External reference
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
10.1517/17460441.2015.1032936 · 2015 · External reference
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
10.1016/s0006-3495(04)74084-9 · 2004 · External reference
10.1021/acs.chemrev.9b00055
10.1021/acs.chemrev.9b00055 · External reference
10.1007/978-1-61779-465-0_20
10.1007/978-1-61779-465-0_20 · External reference
10.1007/978-1-61779-465-0_19
10.1007/978-1-61779-465-0_19 · External reference
Simple Entropy Terms for End-Point Binding Free Energy Calculations
10.1021/acs.jctc.8b00418 · 2018 · External reference
10.1021/ct200153u
10.1021/ct200153u · External reference
Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies
10.1021/ct200163c · 2011 · External reference
Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
10.1039/c7cp07623a · 2018 · External reference
Recent Developments in Free Energy Calculations for Drug Discovery
10.3389/fmolb.2021.712085 · 2021 · External reference
A simple PB/LIE free energy function accurately predicts the peptide binding specificity of the Tiam1 PDZ domain
10.3389/fmolb.2017.00065 · 2017 · External reference
10.1016/j.str.2016.03.026
10.1016/j.str.2016.03.026 · External reference
10.1002/qua.24785
10.1002/qua.24785 · External reference
10.1063/1.1308516
10.1063/1.1308516 · External reference
Molecular Dynamics Simulations of DNA Dimers Based on Replica-Exchange Umbrella Sampling. I. Test of Sampling Efficiency
10.1142/s0219633605001611 · 2005 · External reference
10.1038/s41589-020-00694-2
10.1038/s41589-020-00694-2 · External reference
10.1021/ct100569y
10.1021/ct100569y · External reference
10.1021/acs.jctc.9b00062
10.1021/acs.jctc.9b00062 · External reference
Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures
10.1002/jcc.21415 · 2010 · External reference
Multiscale modeling of biomolecular systems: in serial and in parallel
10.1016/j.sbi.2007.03.004 · 2007 · External reference
10.1063/5.0012320
10.1063/5.0012320 · External reference
Biochemical and Structural Investigation of GnnA in the Lipopolysaccharide Biosynthesis Pathway of Acidithiobacillus ferrooxidans
10.1021/acschembio.0c00791 · 2020 · External reference
10.1074/jbc.ra118.002503
10.1074/jbc.ra118.002503 · External reference
Disruption of the E. coli LptC dimerization interface and characterization of lipopolysaccharide and LptA binding to monomeric LptC
10.1002/pro.3429 · 2018 · External reference
10.1016/j.cpc.2009.05.011
10.1016/j.cpc.2009.05.011 · External reference
10.1146/annurev-physchem-103019-033434
10.1146/annurev-physchem-103019-033434 · External reference
10.1021/acs.jpcb.5b07122
10.1021/acs.jpcb.5b07122 · External reference
10.1021/jp401512z
10.1021/jp401512z · External reference
10.1021/acs.chemrev.8b00384
10.1021/acs.chemrev.8b00384 · External reference
Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections
10.1021/acs.jctc.9b00813 · 2020 · External reference
Unresolved reference
1999 · External reference
