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List of works by Özlem Keskin

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients

scientific article published on 17 January 2019

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients

scientific article published on 17 September 2019

A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway.

scientific article

A comparative molecular dynamics study of methylation state specificity of JMJD2A.

scientific article

A hereditary angioedema screening on an index case: Turkey

scientific article published on 01 September 2019

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications

scientific article

A strategy based on protein-protein interface motifs may help in identifying drug off-targets

scientific article published on 31 July 2012

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

scientific article published on 24 February 2009

Advances in template-based protein docking by utilizing interfaces towards completing structural interactome

scientific article

Allostery and population shift in drug discovery

scientific article published on 29 September 2010

An investigation into respiratory tract viruses in children with acute lower respiratory tract infection or wheezing.

scientific article

Analysis and network representation of hotspots in protein interfaces using minimum cut trees.

scientific article published in August 2010

Analysis of Hot Region Organization in Hub Proteins

article

Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces

scientific article published on 01 September 2018

Androgen receptor-binding sites are highly mutated in prostate cancer

scientific article published on 11 February 2020

Anisotropy of fluctuation dynamics of proteins with an elastic network model

scientific article

Architectures and functional coverage of protein-protein interfaces

scientific article published on 06 May 2008

Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ

scientific article published on 18 July 2018

Autoimmune polyglandular syndrome type 3c with ectodermal dysplasia, immune deficiency and hemolytic-uremic syndrome

scientific article

Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA

scientific article published on 10 January 2020

Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

scientific article published on 17 May 2007

Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions

scientific article published on September 2015

CCRXP: exploring clusters of conserved residues in protein structures

scientific article

COmparisoN of TastES of Available NutriTional integrated or non-integrated formulas for infants older than 1 year of age with cow’s milk allergy: A multicenter, prospective, single blind, cross-sectional observational clinical study (CONTEST Study)

scientific article published in 2022

Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks

scientific article

Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure.

scientific article published in April 2000

Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain

scientific article

Clinical and genetic features of IL12Rb1 deficiency: Single center experience of 18 patients

scientific article

Clinical features and accompanying findings of Pseudo-Bartter Syndrome in cystic fibrosis

scientific article published on 04 May 2020

Comparing interfacial dynamics in protein-protein complexes: an elastic network approach

scientific article

Comparing the effects of fluticasone, anti-IgE and anti-TNF treatments in a chronic asthma model

scientific article

Comparison of full-atomic and coarse-grained models to examine the molecular fluctuations of c-AMP dependent protein kinase

scientific article published on 01 December 2002

Conformational ensembles, signal transduction and residue hot spots: application to drug discovery.

scientific article published on September 2010

Constructing structural networks of signaling pathways on the proteome scale

scientific article published on 09 May 2012

Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level

scientific article published on 01 May 2019

Cystic fibrosis in Turkey: First data from the national registry

scientific article published on 11 November 2019

Developments in integrative modeling with dynamical interfaces

scientific article published on 12 November 2018

Do the leukotriene receptor antagonists work in children with grass pollen-induced allergic rhinitis?

scientific article published on 01 June 2006

Does specific immunotherapy injection cause an increase in bronchial reactivity?

scientific article published in November 2005

Editorial overview: Protein-protein interactions

scientific article published on 26 November 2015

Effects of pentoxifylline on TNF-alpha production by peripheral blood mononuclear cells in patients with nonalcoholic steatohepatitis

scientific article published on 12 April 2007

Embedding Alternative Conformations of Proteins in Protein-Protein Interaction Networks

scientific article published on 01 January 2020

Emerging role of the ubiquitin-proteasome system as drug targets

scientific article published on January 2013

Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions

scientific article

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

scientific article published on 03 August 2017

Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes

scientific article

Evaluation of the utility of atopy patch testing, skin prick testing, and total and specific IgE assays in the diagnosis of cow's milk allergy

scientific article published on 01 May 2005

Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation

scientific article published on 20 May 2019

Exhaled RANTES and interleukin 4 levels after exercise challenge in children with asthma

scientific article published on 01 November 2012

Exhaled TGF-β1 levels before and after an exercise challenge in asthmatic and healthy children, and during exacerbation

scientific article published on 11 November 2019

Expanding the conformational selection paradigm in protein-ligand docking

scientific article published on January 2012

Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale

scientific article published on 30 April 2013

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement

scientific article published on 31 January 2012

Fasting: an important issue in asthma management compliance

scientific article published in September 2006

Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways

scientific article

GTP-Dependent K-Ras Dimerization

scientific article published on 4 June 2015

Genetic associations of the response to inhaled corticosteroids in asthma: a systematic review

scientific article published on 09 January 2019

Genetic associations of the response to inhaled corticosteroids in children during an asthma exacerbation.

scientific article

HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry

scientific article published on 13 February 2020

Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-κB Pathways

scientific article published on 17 October 2019

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues

scientific article

Hot spots in protein-protein interfaces: towards drug discovery.

scientific article published on 02 July 2014

HotPoint: hot spot prediction server for protein interfaces

scientific article published on 5 May 2010

HotRegion: a database of predicted hot spot clusters

scientific article

HotSprint: database of computational hot spots in protein interfaces

scientific article published on 24 October 2007

How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues

scientific article

Human cancer protein-protein interaction network: a structural perspective

scientific article

Human papillomavirus vaccines and cervical cancer: awareness, knowledge, and risk perception among Turkish undergraduate students

scientific article published on March 2015

Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs

scientific article published on 10 January 2012

IL-12Rβ1 deficiency: mutation update and description of the IL12RB1 variation database

scientific article

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy.

scientific article

Identification of interconnected markers for T-cell acute lymphoblastic leukemia

scientific article published on 15 July 2013

Identification of potential inhibitors of human methionine aminopeptidase (type II) for cancer therapy: Structure-based virtual screening, ADMET prediction and molecular dynamics studies

scientific article published on 02 March 2020

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

scientific article published on 01 December 2009

Immunophenotypic analysis of lymphocyte subsets in newborns with biotinidase deficiency

scientific article published on 20 November 2020

Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase

scientific article published on 18 July 2008

Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer

scientific article

Interaction prediction and classification of PDZ domains.

scientific article

Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase

scientific article

Is ovarian volume a good predictor to determine metabolic syndrome development in polycystic ovary patients

scientific article published on 11 February 2019

Is the CD14 C159T polymorphism effective in the development of secondary amyloidosis in Familial Mediterranean fever?

scientific article published on 23 December 2006

Is there any difference in the use of complementary and alternative therapies in patients asthma and COPD? A cross-sectional survey

scientific article

K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target?

scientific article published on 12 February 2016

Kindlin3-dependent CD11b/CD18-integrin activation is required for potentiation of neutrophil cytotoxicity by CD47-SIRPα checkpoint disruption

scientific article published on 22 December 2020

Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers

scientific article

Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing

scientific article published on 01 January 2019

Modeling protein assemblies in the proteome

scientific article published on 20 January 2014

Molecular Mechanisms of Chaperonin GroEL−GroES Function ⬇️

scientific article published on January 15, 2002

Molecular motions and conformational changes of HPPK.

scientific article

Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study

scientific article

Most children who are allergic to cow's milk tolerate yogurt

scientific article published on 09 August 2018

Network-based strategies can help mono- and poly-pharmacology drug discovery: a systems biology view

scientific article published on January 2014

Non-redundant unique interface structures as templates for modeling protein interactions

scientific article published on 27 January 2014

Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling

scientific article published on 10 January 2020

Oxidative stress and genetic and epidemiologic determinants of oxidant injury in childhood asthma

scientific article published on 01 November 2006

PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization.

scientific article published on 25 May 2017

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps

scientific article

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum.

scientific article published in January 2018

PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes

scientific article

PRISM: protein interactions by structural matching

scientific article

PRISM: protein-protein interaction prediction by structural matching

scientific article published on January 2008

Packing of sidechains in low-resolution models for proteins

scientific article

Perceptions of Parents and Physicians Concerning the Childhood Asthma Control Test ⬇️

scientific article published on September 7, 2012

Plasma membrane regulates Ras signaling networks

scientific article published on October 2015

Poppy seed allergy: a case report and review of the literature

scientific article

Predicting Hospitalization in Children with Acute Asthma ⬇️

scientific article published on January 16, 2013

Predicting Protein-Protein Interactions from the Molecular to the Proteome Level

scientific article published on 13 April 2016

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

scientific article published on 11 August 2011

Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information

scientific article published on January 2017

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces

scientific article (publication date: 26 April 2005)

Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces

scientific article published on 13 May 2011

Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation

scientific article published on 23 October 2015

Principles of protein-protein interactions: what are the preferred ways for proteins to interact?

scientific article published on 21 March 2008

Protective effects of vitamin D on ischemia-reperfusion injury of the ovary in a rat model

scientific article

Protein interactions and fluctuations in a proteomic network using an elastic network model.

scientific article

Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

scientific article published on 18 September 2008

Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking

scientific article

Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach

scientific article

Protein-protein interfaces integrated into interaction networks: implications on drug design.

scientific article published on January 2012

Proteins with similar architecture exhibit similar large-scale dynamic behavior

scientific article

Ras Conformational Ensembles, Allostery, and Signaling

scientific article published on 27 January 2016

Reaction path analysis for demethylation process of histone tail lysine residues

Relating molecular flexibility to function: a case study of tubulin

scientific article

Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations

scientific article published on 9 February 2017

Relationship between exhaled leukotriene and 8-isoprostane levels and asthma severity, asthma control level, and asthma control test score

scientific article published on 21 December 2012

Relationships between amino acid sequence and backbone torsion angle preferences.

scientific article

Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations.

scientific article published on 28 January 2008

Sciatic nerve hypertrophy with Klippel-Trenaunay syndrome: a case report

scientific article published in January 2015

Similar binding sites and different partners: implications to shared proteins in cellular pathways

scientific article published on March 2007

Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP

scientific article

Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patients.

scientific article

Structural cooperativity in histone H3 tail modifications

scientific article published on 19 October 2011

Structural pathways of cytokines may illuminate their roles in regulation of cancer development and immunotherapy.

scientific article

TRAF3 signaling: Competitive binding and evolvability of adaptive viral molecular mimicry.

scientific article published on 18 May 2016

Taming Oncogenic Signaling at Protein Interfaces: Challenges and Opportunities.

scientific article

The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway

scientific article

The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas

scientific article

The binding affinities of proteins interacting with the PDZ domain of PICK1.

scientific article published on 24 February 2012

The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins

scientific article

The distinct genetic pattern of ALS in Turkey and novel mutations.

scientific article published on 10 January 2015

The effect of CD14-c159T genotypes on the cytokine response to endotoxin by peripheral blood mononuclear cells from asthmatic children

scientific article

The effect of montelukast on early-life wheezing: A randomized, double-blinded placebo-controlled study.

scientific article

The effects of grass pollen allergoid immunotherapy on clinical and immunological parameters in children with allergic rhinitis

scientific article published on 01 September 2006

The efficacy of single-high dose inhaled corticosteroid versus oral prednisone treatment on exhaled leukotriene and 8-isoprostane levels in mild to moderate asthmatic children with asthma exacerbation.

scientific article published on 26 August 2015

The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology

scientific article published on 22 April 2016

The relationship between serum vitamin D level and asthma

scientific article published on 04 July 2019

The role of SCCA1 in asthma related physiological events in the airway epithelium and the effect of promoter variants on asthma and gene function.

scientific article published on 28 November 2012

The structural network of Interleukin-10 and its implications in inflammation and cancer

scientific article

The structural network of inflammation and cancer: merits and challenges.

scientific article published on 24 May 2013

The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer

scientific article (publication date: February 2014)

Topological properties of protein interaction networks from a structural perspective

scientific article published on December 2008

Topological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases

Towards drugs targeting multiple proteins in a systems biology approach

scientific article published in January 2007

Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example ⬇️

scientific article published in December 2009

Transient protein-protein interactions.

scientific article published on 15 June 2011

Trends in the Frequency of HLA DR-DQ Haplotypes Among Children and Adolescents with Type 1 Diabetes Mellitus in the Southeast Region of Turkey ⬇️

scientific article published on December 1, 2012

Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2.

scientific article published on 22 January 2018

Unusual presentation: pulmonary hemosiderosis with celiac disease and retinitis pigmentosa in a child

scientific article published on 18 February 2011

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