Lista de obras - Yiannis N Kaznessis - Dominio Público Uruguay

A Review of Methods for Computational Prediction of Blood-Brain Partitioning

artículo científico publicado en 2005

A closure scheme for chemical master equations

artículo científico publicado en 2013

A linearization method for probability moment equations

artículo científico publicado en 2018

A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes.

artículo científico publicado en 2005

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions

artículo científico publicado en 2005

An adaptive time step scheme for a system of stochastic differential equations with multiple multiplicative noise: chemical Langevin equation, a proof of concept.

artículo científico publicado en 2008

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks

artículo científico publicado en 2005

Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics.

artículo científico publicado en 2011

Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts

artículo científico publicado en 2017

Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli

artículo científico publicado en 2009

Antimicrobial peptides targeting Gram-negative pathogens, produced and delivered by lactic acid bacteria.

artículo científico publicado en 2013

Bacterial sugar utilization gives rise to distinct single-cell behaviours

artículo científico publicado en 2014

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

artículo científico publicado en 2007

Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium

artículo científico publicado en 2017

Chloride-Inducible Expression Vector for Delivery of Antimicrobial Peptides Targeting Antibiotic-Resistant Enterococcus faecium

artículo científico publicado en 2015

Computational methods in synthetic biology

artículo científico publicado en 2009

Computational studies of protegrin antimicrobial peptides: a review.

artículo científico publicado en 2010

Computer-aided design of modular protein devices: Boolean AND gene activation.

artículo científico publicado en 2006

Concentration and Size Dependence of Dielectric Strength and Dielectric Relaxation of Polymers in Solutions of a ϑ Solvent via Molecular Dynamics Simulations

artículo científico publicado en 1999

Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy

artículo científico publicado en 2004

Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis

artículo científico publicado en 2011

Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: predicting experimental toxicity.

artículo científico publicado en 2008

Corrigendum to “Structure of the antimicrobial β-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation” [Biochim. Biophys. Acta 1768 (2007) 509–520]

artículo científico publicado en 2010

Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model

artículo científico publicado en 2009

Development of a new pharmacophore model that discriminates active compstatin analogs

artículo científico publicado en 2008

Dimerization of protegrin-1 in different environments.

artículo científico publicado en 2010

Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions

artículo científico publicado en 2006

Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant in the intestinal tract

scholarly article by Kathryn G Geldart et al published September 2018 in Bioengineering & Translational Medicine

Enterocin A mutants identified by saturation mutagenesis enhance potency towards vancomycin-resistant Enterococci

artículo científico publicado en 2015

Forward engineering of synthetic bio-logical AND gates

artículo científico publicado en 2009

Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor.

artículo científico publicado en 2017

Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer

artículo científico publicado en 2010

How can a beta-sheet peptide be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of protegrin-1 in micelles.

artículo científico publicado en 2006

Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination.

artículo científico publicado en 2005

Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations.

artículo científico publicado en 2018

Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations

artículo científico publicado en 2016

Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator.

artículo científico publicado en 2014

Mathematical models in biology: from molecules to life ⬇️

artículo científico publicado el 18 de febrero de 2011

Maximum Entropy Prediction of Non-Equilibrium Stationary Distributions for Stochastic Reaction Networks with Oscillatory Dynamics

scientific article published on 22 May 2017

Model reduction of multiscale chemical langevin equations: a numerical case study.

artículo científico publicado en 2009

Model-driven designs of an oscillating gene network

artículo científico publicado en 2005

Modeling Osmotic Lysis of Cells by Antimicrobial Peptides: Transient Diffusion of Ions and Osmotically-driven Flow

artículo científico publicado en 2009

Models for synthetic biology

artículo científico publicado en 2007

Modified lactic acid bacteria detect and inhibit multiresistant enterococci.

artículo científico publicado en 2014

Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

artículo científico publicado en 2005

Molecular dynamics simulations of dielectric relaxation of concentrated polymer solutions

artículo científico publicado en 1999

Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: what do point mutations achieve?

artículo científico publicado en 2005

Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle: insights into host-cell toxicity

artículo científico publicado en 2005

Molecular dynamics simulations of three protegrin-type antimicrobial peptides: interplay between charges at the termini, β-sheet structure and amphiphilic interactions ⬇️

artículo científico publicado el 1 de agosto de 2007

Molecular simulations of antimicrobial peptides

artículo científico publicado en 2010

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

artículo científico publicado en 2006

Multiscale Models of Antibiotic Probiotics.

artículo científico publicado en 2014

Multiscale models of the antimicrobial peptide protegrin-1 on gram-negative bacteria membranes

artículo científico publicado en 2012

Multispecies activity screening of microcin J25 mutants yields antimicrobials with increased specificity toward pathogenic Salmonella species relative to human commensal Escherichia coli

artículo científico publicado en 2018

Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency

artículo científico publicado en 2010

Numerical simulation of stochastic gene circuits

artículo científico publicado en 2005

On Differences between Deterministic and Stochastic Models of Chemical Reactions: Schlögl Solved with ZI-Closure

artículo científico publicado en 2018

On a theory of stability for nonlinear stochastic chemical reaction networks.

artículo científico publicado en 2015

On the nature of antimicrobial activity: a model for protegrin-1 pores

artículo científico publicado en 2008

Optimization of a stochastically simulated gene network model via simulated annealing.

artículo científico publicado en 2006

Path-integral method for predicting relative binding affinities of protein-ligand complexes.

artículo científico publicado en 2009

Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions

artículo científico publicado en 2005

Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore

artículo científico publicado en 2009

Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water ⬇️

artículo científico publicado el 1 de agosto de 2001

Prediction of distant residue contacts with the use of evolutionary information.

artículo científico publicado en 2005

Protegrin structure-activity relationships: using homology models of synthetic sequences to determine structural characteristics important for activity.

artículo científico publicado en 2005

Rare loss-of-function mutation in complement component C3 provides insight into molecular and pathophysiological determinants of complement activity

artículo científico publicado en 2015

Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

artículo científico publicado en 2009

Residue conservation information for generating near-native structures in protein-protein docking.

artículo científico publicado en 2006

Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin

artículo científico publicado en 2006

Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations.

artículo científico publicado en 2008

Simulation of the N-terminus of HIV-1 glycoprotein 41000 fusion peptide in micelles

artículo científico publicado en 2005

Simulations of zwitterionic and anionic phospholipid monolayers

artículo científico publicado en 2002

Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks

artículo científico publicado en 2014

Solving Stochastic Reaction Networks with Maximum Entropy Lagrange Multipliers

artículo científico publicado en 2018

Specific mode of interaction between components of model pulmonary surfactants using computer simulations.

artículo científico publicado en 2002

Statistical Thermodynamics and Stochastic Kinetics

artículo científico publicado en 2009

Stochastic model reduction using a modified Hill-type kinetic rate law.

artículo científico publicado en 2012

Stochastic simulations of a synthetic bacteria-yeast ecosystem

artículo científico publicado en 2012

Stochastic simulations of the tetracycline operon

artículo científico publicado en 2011

Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

artículo científico publicado en 2006

Structure-Function Analysis of the Two-Peptide Bacteriocin Plantaricin EF

artículo científico publicado en 2016

Structure-kinetic relationship analysis of the therapeutic complement inhibitor compstatin

artículo científico publicado en 2009

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

artículo científico publicado en 2010

SynBioSS: the synthetic biology modeling suite

artículo científico publicado en 2008

Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

artículo científico publicado en 2007

Thermodynamic Analysis of Protegrin-1 insertion and Permeation through a Lipid Bilayer

artículo científico publicado en 2011

Thermodynamic analysis of protegrin-1 insertion and permeation through a lipid bilayer

artículo científico publicado en 2011

Trade-offs in engineering sugar utilization pathways for titratable control

artículo científico publicado en 2014

Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER

scientific article published on 01 August 2007

pMPES: A Modular Peptide Expression System for the Delivery of Antimicrobial Peptides to the Site of Gastrointestinal Infections Using Probiotics

artículo científico publicado en 2016

Lista de obras de Yiannis N Kaznessis

A Review of Methods for Computational Prediction of Blood-Brain Partitioning

A closure scheme for chemical master equations

A linearization method for probability moment equations

A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes.

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions

An adaptive time step scheme for a system of stochastic differential equations with multiple multiplicative noise: chemical Langevin equation, a proof of concept.

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks

Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics.

Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts

Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli

Antimicrobial peptides targeting Gram-negative pathogens, produced and delivered by lactic acid bacteria.

Bacterial sugar utilization gives rise to distinct single-cell behaviours

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium

Chloride-Inducible Expression Vector for Delivery of Antimicrobial Peptides Targeting Antibiotic-Resistant Enterococcus faecium

Computational methods in synthetic biology

Computational studies of protegrin antimicrobial peptides: a review.

Computer-aided design of modular protein devices: Boolean AND gene activation.

Concentration and Size Dependence of Dielectric Strength and Dielectric Relaxation of Polymers in Solutions of a ϑ Solvent via Molecular Dynamics Simulations

Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy

Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis

Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: predicting experimental toxicity.

Corrigendum to “Structure of the antimicrobial β-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation” [Biochim. Biophys. Acta 1768 (2007) 509–520]

Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model

Development of a new pharmacophore model that discriminates active compstatin analogs

Dimerization of protegrin-1 in different environments.

Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions

Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant in the intestinal tract

Enterocin A mutants identified by saturation mutagenesis enhance potency towards vancomycin-resistant Enterococci

Forward engineering of synthetic bio-logical AND gates

Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor.

Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer

How can a beta-sheet peptide be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of protegrin-1 in micelles.

Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination.

Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations.

Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations

Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator.

Mathematical models in biology: from molecules to life ⬇️

Maximum Entropy Prediction of Non-Equilibrium Stationary Distributions for Stochastic Reaction Networks with Oscillatory Dynamics

Model reduction of multiscale chemical langevin equations: a numerical case study.

Model-driven designs of an oscillating gene network

Modeling Osmotic Lysis of Cells by Antimicrobial Peptides: Transient Diffusion of Ions and Osmotically-driven Flow

Models for synthetic biology

Modified lactic acid bacteria detect and inhibit multiresistant enterococci.

Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

Molecular dynamics simulations of dielectric relaxation of concentrated polymer solutions

Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: what do point mutations achieve?

Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle: insights into host-cell toxicity

Molecular dynamics simulations of three protegrin-type antimicrobial peptides: interplay between charges at the termini, β-sheet structure and amphiphilic interactions ⬇️

Molecular simulations of antimicrobial peptides

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

Multiscale Models of Antibiotic Probiotics.

Multiscale models of the antimicrobial peptide protegrin-1 on gram-negative bacteria membranes

Multispecies activity screening of microcin J25 mutants yields antimicrobials with increased specificity toward pathogenic Salmonella species relative to human commensal Escherichia coli

Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency

Numerical simulation of stochastic gene circuits

On Differences between Deterministic and Stochastic Models of Chemical Reactions: Schlögl Solved with ZI-Closure

On a theory of stability for nonlinear stochastic chemical reaction networks.

On the nature of antimicrobial activity: a model for protegrin-1 pores

Optimization of a stochastically simulated gene network model via simulated annealing.

Path-integral method for predicting relative binding affinities of protein-ligand complexes.

Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions

Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore

Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water ⬇️

Prediction of distant residue contacts with the use of evolutionary information.

Protegrin structure-activity relationships: using homology models of synthetic sequences to determine structural characteristics important for activity.

Rare loss-of-function mutation in complement component C3 provides insight into molecular and pathophysiological determinants of complement activity

Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

Residue conservation information for generating near-native structures in protein-protein docking.

Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin

Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations.

Simulation of the N-terminus of HIV-1 glycoprotein 41000 fusion peptide in micelles

Simulations of zwitterionic and anionic phospholipid monolayers

Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks

Solving Stochastic Reaction Networks with Maximum Entropy Lagrange Multipliers

Specific mode of interaction between components of model pulmonary surfactants using computer simulations.

Statistical Thermodynamics and Stochastic Kinetics

Stochastic model reduction using a modified Hill-type kinetic rate law.

Stochastic simulations of a synthetic bacteria-yeast ecosystem