Lista de obras - Syma Khalid - Dominio Público Uruguay

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

scientific article published on 17 May 2018

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

artículo científico publicado en 2011

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

scientific article published on 20 November 2020

An accurate in vitro model of the E. coli envelope.

artículo científico publicado en 2015

Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned?

artículo científico publicado en 2018

Bookshelf: a simple curation system for the storage of biomolecular simulation data

artículo científico publicado en 2010

Both interaction surfaces within cohesin's hinge domain are essential for its stable chromosomal association

artículo científico publicado en 2010

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

artículo científico publicado en 2008

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

scientific article published on 20 October 2006

Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations.

artículo científico publicado en 2018

Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: a molecular dynamics simulation study

artículo científico publicado en 2012

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study.

artículo científico publicado en 2008

Correction to "Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm"

artículo científico publicado en 2018

Correction to Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

artículo científico publicado en 2017

DNA and lipid bilayers: self-assembly and insertion

artículo científico publicado en 2008

DNA lipoplexes: formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation

artículo científico publicado en 2010

DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants

artículo científico publicado en 2015

Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm

scientific article published on 06 July 2018

Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles

artículo científico publicado en 2019

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

artículo científico publicado en 2016

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores

artículo científico publicado en 2018

Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes.

artículo científico publicado en 2011

Enantiomeric resolution of supramolecular helicates with different surface topographies

artículo científico publicado en 2006

Encapsulated membrane proteins: A simplified system for molecular simulation.

artículo científico publicado en 2016

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

artículo científico publicado el 24 de febrero de 2011

Free-energy calculations reveal the subtle differences in the interactions of DNA bases with α-hemolysin.

artículo científico publicado en 2015

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

artículo científico publicado en 2016

Influence of surface shape on DNA binding of bimetallo helicates.

artículo científico publicado en 2007

Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state--Implications for the Hepatitis C virus life cycle.

artículo científico

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

artículo científico publicado en 2015

Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: differential binding of P and M helical enantiomers.

artículo científico publicado en 2002

It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli

artículo científico publicado en 2017

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

artículo científico publicado en 2015

Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes

artículo científico publicado en 2016

Molecular Dynamics Simulations Reveal the Conformational Flexibility of Lipid II and Its Loose Association with the Defensin Plectasin in the Staphylococcus aureus Membrane.

artículo científico publicado en 2016

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

artículo científico publicado en 2012

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

artículo científico publicado en 2015

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

artículo científico publicado en 2011

Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis.

artículo científico publicado en 2006

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

artículo científico publicado en 2020

Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study

artículo científico publicado en 2007

Movement of Arginine through OprD: The Energetics of Permeation and the Role of Lipopolysaccharide in Directing Arginine to the Protein

scientific article published on 19 March 2019

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

artículo científico publicado en 2016

On the ability of PAMAM dendrimers and dendrimer/DNA aggregates to penetrate POPC model biomembranes

artículo científico publicado en 2010

Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints

scientific article published on 21 March 2019

Outer membrane protein G: Engineering a quiet pore for biosensing

artículo científico publicado en 2008

Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers.

artículo científico publicado en 2011

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes

artículo científico publicado en 2017

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

artículo científico publicado en 2017

Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations

artículo científico publicado en 2019

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.

artículo científico publicado en 2008

Shape effects on the activity of synthetic major-groove binding ligands

artículo científico publicado en 2006

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

scientific article published on 01 April 2006

Stability and membrane orientation of the fukutin transmembrane domain: a combined multiscale molecular dynamics and circular dichroism study

artículo científico publicado en 2010

Structural basis for Mep2 ammonium transceptor activation by phosphorylation.

artículo científico publicado en 2016

The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile.

artículo científico publicado en 2016

The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations

artículo científico publicado en 2014

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

artículo científico

The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization

artículo científico publicado en 2018

Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes

artículo científico publicado en 2017

Lista de obras de Syma Khalid

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

An accurate in vitro model of the E. coli envelope.

Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned?

Bookshelf: a simple curation system for the storage of biomolecular simulation data

Both interaction surfaces within cohesin's hinge domain are essential for its stable chromosomal association

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations.

Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: a molecular dynamics simulation study

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study.

Correction to "Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm"

Correction to Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

DNA and lipid bilayers: self-assembly and insertion

DNA lipoplexes: formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation

DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants

Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm

Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores

Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes.

Enantiomeric resolution of supramolecular helicates with different surface topographies

Encapsulated membrane proteins: A simplified system for molecular simulation.

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

Free-energy calculations reveal the subtle differences in the interactions of DNA bases with α-hemolysin.

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

Influence of surface shape on DNA binding of bimetallo helicates.

Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state--Implications for the Hepatitis C virus life cycle.

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: differential binding of P and M helical enantiomers.

It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes

Molecular Dynamics Simulations Reveal the Conformational Flexibility of Lipid II and Its Loose Association with the Defensin Plectasin in the Staphylococcus aureus Membrane.

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis.

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study

Movement of Arginine through OprD: The Energetics of Permeation and the Role of Lipopolysaccharide in Directing Arginine to the Protein

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

On the ability of PAMAM dendrimers and dendrimer/DNA aggregates to penetrate POPC model biomembranes

Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints

Outer membrane protein G: Engineering a quiet pore for biosensing

Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers.

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.

Shape effects on the activity of synthetic major-groove binding ligands

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

Stability and membrane orientation of the fukutin transmembrane domain: a combined multiscale molecular dynamics and circular dichroism study

Structural basis for Mep2 ammonium transceptor activation by phosphorylation.

The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile.

The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization

Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes