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List of works by Serdar Kuyucak

A model of calcium channels

scientific article published on 01 December 2000

A potent and selective peptide blocker of the Kv1.3 channel: prediction from free-energy simulations and experimental confirmation

scientific article

A simple, parameter-free method for computing solvation free energies of ions

scientific article published on 01 February 2019

Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl

scientific article published on 01 May 2011

Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints ⬇️

scientific article published on May 18, 2011

Affinity and selectivity of ShK toxin for the Kv1 potassium channels from free energy simulations

scientific article published on 16 April 2012

Analytical solutions of Poisson's equation for realistic geometrical shapes of membrane ion channels

scientific article

Brownian dynamics study of ion transport in the vestibule of membrane channels

scientific article

Changes in the kinetics and conductance of N-methyl-D-aspartate (NMDA)-receptor activated single channels with temperature

scientific article

Charge state of the fast gate in chloride channels: insights from electrostatic calculations in a schematic model

scientific article published in November 2007

Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics

scientific article

Computational study of aggregation mechanism in human lysozyme[D67H]

scientific article

Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations.

scientific article

Continuum electrostatics fails to describe ion permeation in the gramicidin channel

scientific article

Developing a Comparative Docking Protocol for the Prediction of Peptide Selectivity Profiles: Investigation of Potassium Channel Toxins ⬇️

scientific article published on February 6, 2012

Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels

scientific article

Dissociation of NaCl in water from ab initio molecular dynamics simulations

scientific article published on 01 March 2010

Electromagnetic properties of low-excitation states in 191Ir and 193Ir and supersymmetry schemes

Elucidation of the Role of a Conserved Methionine in Glutamate Transporters and Its Implication for Force Fields.

scientific article published on 25 September 2017

Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations

scientific article published on 13 March 2006

Energy barrier presented to ions by the vestibule of the biological membrane channel

scientific article

Force fields for simulating the interaction of surfaces with biological molecules

scientific article

Free energy simulations of ligand binding to the aspartate transporter Glt(Ph).

scientific article published on 15 November 2011

Free energy simulations of single and double ion occupancy in gramicidin A

scientific article published on 01 March 2007

Functional properties of threefold and fourfold channels in ferritin deduced from electrostatic calculations

scientific article

Gramicidin A channel as a test ground for molecular dynamics force fields

scientific article

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

scientific article published on 01 November 2012

Mechanisms of permeation and selectivity in calcium channels

scientific article

Modeling diverse range of potassium channels with Brownian dynamics.

scientific article

Modelling the interactions between animal venom peptides and membrane proteins

scientific article published in August 2017

Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex ⬇️

scientific article published on February 18, 2013

Molecular dynamics estimates of ion diffusion in model hydrophobic and KcsA potassium channels.

scientific article

Molecular dynamics study of the KcsA potassium channel

scientific article

Permeation models and structure-function relationships in ion channels

scientific article

Permeation of ions across the potassium channel: Brownian dynamics studies

scientific article

Physics of Ion Channels ⬇️

scientific article published on December 1, 2003

Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling

scientific article published on 01 April 2008

Recent advances in ion channel research

scientific article

Reservoir boundaries in Brownian dynamics simulations of ion channels

scientific article

Role of protein flexibility in ion permeation: a case study in gramicidin A.

scientific article published on 13 January 2006

Role of the dielectric constants of membrane proteins and channel water in ion permeation

scientific article

Study of ionic currents across a model membrane channel using Brownian dynamics

scientific article

Temperature dependence of conductivity in electrolyte solutions and ionic channels of biological membranes

scientific article published in September 1994

Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics.

scientific article

Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus brownian dynamics

scientific article

Why the Drosophila Shaker K+ Channel Is Not a Good Model for Ligand Binding to Voltage-Gated Kv1 Channels ⬇️

scientific article published on February 20, 2013

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