User profiles for A. Hacisuleyman
Aysima HacisuleymanDepartment of Computational Biology, UNIL Verified email at unil.ch Cited by 154 |
[HTML][HTML] Entropy transfer between residue pairs and allostery in proteins: quantifying allosteric communication in ubiquitin
A Hacisuleyman, B Erman - PLoS computational biology, 2017 - journals.plos.org
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property
of all proteins. Here, we develop a computational method that can determine and quantify …
of all proteins. Here, we develop a computational method that can determine and quantify …
Prediction of allosteric communication pathways in proteins
Motivation Allostery in proteins is an essential phenomenon in biological processes. In this
article, we present a computational model to predict paths of maximum information transfer …
article, we present a computational model to predict paths of maximum information transfer …
Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions
A Hacisuleyman, B Erman - Proteins: Structure, Function, and …, 2017 - Wiley Online Library
A fast and approximate method of generating allosteric communication landscapes in
proteins is presented by using Schreiber's entropy transfer concept in combination with the …
proteins is presented by using Schreiber's entropy transfer concept in combination with the …
Synchronous and asynchronous response in dynamically perturbed proteins
We present a dynamic perturbation-response model of proteins based on the Gaussian
Network Model, where a residue is perturbed periodically, and the dynamic response of other …
Network Model, where a residue is perturbed periodically, and the dynamic response of other …
SARS-Cov-2 delta variant decreases nanobody binding and ACE2 blocking effectivity
The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant
comprises several mutations on the receptor-binding domain (RBD Delta ) of its spike …
comprises several mutations on the receptor-binding domain (RBD Delta ) of its spike …
Binding mechanism of neutralizing nanobodies targeting SARS-CoV-2 spike glycoprotein
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human cells upon
binding of its spike (S) glycoproteins to ACE2 receptors. Several nanobodies neutralize SARS…
binding of its spike (S) glycoproteins to ACE2 receptors. Several nanobodies neutralize SARS…
Synergy and anti‐cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS‐RGL1
A Hacisuleyman, B Erman - Proteins: Structure, Function, and …, 2023 - Wiley Online Library
This study focuses on investigating the effects of an oncogenic mutation (G12V) on the stability
and interactions within the KRAS‐RGL1 protein complex. The KRAS‐RGL1 complex is of …
and interactions within the KRAS‐RGL1 protein complex. The KRAS‐RGL1 complex is of …
ModiBodies: A computational method for modifying nanobodies in nanobody-antigen complexes to improve binding affinity and specificity
A Hacisuleyman, B Erman - Journal of Biological Physics, 2020 - Springer
Nanobodies are special derivatives of antibodies, which consist of single domain fragments.
They have become of considerable interest as next-generation biotechnological tools for …
They have become of considerable interest as next-generation biotechnological tools for …
Information flow and allosteric communication in proteins
A Hacisuleyman, B Erman - The Journal of Chemical Physics, 2022 - pubs.aip.org
Based on Schreiber’s work on transfer entropy, a molecular theory of nonlinear information
transfer between residue pairs in proteins is developed. The joint distribution function for …
transfer between residue pairs in proteins is developed. The joint distribution function for …
Fine tuning rigid body docking results using the Dreiding force field: A computational study of 36 known nanobody‐protein complexes
A Hacisuleyman, B Erman - Proteins: Structure, Function, and …, 2023 - Wiley Online Library
This paper aims to understand the binding strategies of a nanobody‐protein pair by
studying known complexes. Rigid body protein–ligand docking programs produce several …
studying known complexes. Rigid body protein–ligand docking programs produce several …