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List of works by Attila Gursoy

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 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 ontology for collaborative construction and analysis of cellular pathways.

scientific article published on February 2004

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

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

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

scientific article published on 10 January 2020

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

scientific article

Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins.

scientific article

Conformational energies and entropies of peptides, and the peptide-protein binding problem.

scientific article

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

Developments in integrative modeling with dynamical interfaces

scientific article published on 12 November 2018

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

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

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

Folding dynamics of proteins from denatured to native state: principal component analysis.

scientific article published in January 2004

GTP-Dependent K-Ras Dimerization

scientific article published on 4 June 2015

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 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

Human cancer protein-protein interaction network: a structural perspective

scientific article

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

scientific article published on 10 January 2012

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

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

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

scientific article published on 12 February 2016

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

scientific article

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

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

Plasma membrane regulates Ras signaling networks

scientific article published on October 2015

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

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

scientific article published on January 2012

Ras Conformational Ensembles, Allostery, and Signaling

scientific article published on 27 January 2016

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

scientific article published on 9 February 2017

Relationships between amino acid sequence and backbone torsion angle preferences.

scientific article

Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence

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

scientific article published on 22 April 2016

The structural basis of Akt PH domain interaction with calmodulin

scientific article published on 26 March 2021

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

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

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

VitAL: Viterbi algorithm for de novo peptide design

scientific article

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