List of works - Ora Schueler-Furman

A benchmark testing ground for integrating homology modeling and protein docking

scientific article

A model of anthrax toxin lethal factor bound to protective antigen.

scientific article

Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: a common paradigm.

scientific article published on 7 October 2011

Application of asymmetric statistical potentials to antibody-protein docking

scientific article

Autophosphorylation Activates Dictyostelium Myosin II Heavy Chain Kinase A by Providing a Ligand for an Allosteric Binding Site in the -Kinase Domain

scientific article

Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?

scientific article

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.

scientific article published on 18 April 2017

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking

scientific article published on 06 March 2020

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

scientific article

Computational approaches to investigating allostery

scientific article published on 5 September 2016

Conserved residue clustering and protein structure prediction.

scientific article

Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface

scientific article

Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server

scientific article

Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions

scientific article published on 17 October 2013

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

scientific article

Druggable protein-protein interactions--from hot spots to hot segments.

scientific article published on 31 October 2013

Encounter complexes and dimensionality reduction in protein-protein association

scientific article published on 08 April 2014

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

scientific article published on 29 November 2021

Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation

scientific article

Evolving dual targeting of a prokaryotic protein in yeast.

scientific article published on 5 March 2013

Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins.

scientific article

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

scientific article

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility

scientific article published on 21 December 2016

Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals

scholarly article

Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family

scientific article

FunHunt: model selection based on energy landscape characteristics.

scientific article

Funnel hunting in a rough terrain: learning and discriminating native energy funnels.

scientific article

Harnessing protein folding neural networks for peptide–protein docking

scientific article published on 10 January 2022

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.

scientific article published on 27 December 2017

Host FIH-Mediated Asparaginyl Hydroxylation of Translocated Legionella pneumophila Effectors

scientific article published on 06 March 2017

Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity

scientific article

Identifying a common molecular mechanism for inhibition of MITF and STAT3 by PIAS3.

scientific article published on 20 December 2005

Improved side-chain modeling for protein-protein docking

scientific article

In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2

scientific article published on 12 July 2012

Indirect ELISA-based approach for comparative measurement of high-affinity cohesin-dockerin interactions.

scientific article published in November 2012

Is GAS1 a co-receptor for the GDNF family of ligands?

scientific article

MYORG is associated with recessive primary familial brain calcification

scientific article published on 15 November 2018

Measurements of Relative Binding of Cohesin and Dockerin Mutants Using an Advanced ELISA Technique for High-Affinity Interactions

scientific article published on January 1, 2012

Minimizing and learning energy functions for side-chain prediction.

scientific article

Mitochondrial complex IV deficiency, caused by mutated COX6B1, is associated with encephalomyopathy, hydrocephalus and cardiomyopathy

scientific article

Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind

scientific article

Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45

scientific article published on 31 December 2019

Modeling peptide-protein interactions

scientific article published in January 2012

Molecular pathogenesis of human CD59 deficiency

scientific article published on 26 October 2018

Myelin-associated glycoprotein gene mutation causes Pelizaeus-Merzbacher disease-like disorder

scientific journal article

Parkin Somatic Mutations Link Melanoma and Parkinson's Disease

scientific article

Pathogens use structural mimicry of native host ligands as a mechanism for host receptor engagement

scientific article published on July 2013

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how.

scientific article published on 15 October 2013

Peptiderive server: derive peptide inhibitors from protein-protein interactions

scientific article

Phosphorylation of the WWOX Protein Regulates Its Interaction with p73

scientific article published on 17 March 2020

Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells

scientific article

Progress in modeling of protein structures and interactions

scientific article

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility

scientific article

Protein-peptide docking: opportunities and challenges.

scientific article published on 4 May 2018

Protein-protein docking predictions for the CAPRI experiment

scientific article (publication date: July 2003)

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

scientific article (publication date: August 2003)

Rapid sampling of molecular motions with prior information constraints

scientific article (publication date: February 2009)

Rationally Designed Macrocyclic Peptides as Synergistic Agonists of LPS-Induced Inflammatory Response

scientific article

Relacin, a novel antibacterial agent targeting the Stringent Response

scientific article

Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors

scientific article

Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions

scientific article

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

scientific article

RosettaDock in CAPRI rounds 6-12

scientific article (publication date: December 2007)

Structural basis for UFM1 transfer from UBA5 to UFC1

scientific article published on 29 September 2021

Structure-Based Identification of HDAC8 Non-histone Substrates

scientific article published on March 2016

Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates

Sub-angstrom modeling of complexes between flexible peptides and globular proteins.

scientific article published in July 2010

The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK.

scientific article published in March 2011

The SV40 capsid is stabilized by a conserved pentapeptide hinge of the major capsid protein VP1.

scientific article

The structural basis of peptide-protein binding strategies.

scientific article

The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite

scientific article published on December 2007

Trans protein splicing of cyanobacterial split inteins in endogenous and exogenous combinations.

scientific article

Ubiquitination and degradation of the inhibitors of NF-kappaB

scientific article

Versatile communication strategies among tandem WW domain repeats

scientific article

Yeast aconitase mitochondrial import is modulated by interactions of its C and N terminal domains and Ssa1/2 (Hsp70).

scientific article published on 12 April 2018

c-Abl phosphorylates E6AP and regulates its E3 ubiquitin ligase activity

scientific article published on 26 April 2013

List of works by Ora Schueler-Furman

A benchmark testing ground for integrating homology modeling and protein docking

A model of anthrax toxin lethal factor bound to protective antigen.

Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: a common paradigm.

Application of asymmetric statistical potentials to antibody-protein docking

Autophosphorylation Activates Dictyostelium Myosin II Heavy Chain Kinase A by Providing a Ligand for an Allosteric Binding Site in the -Kinase Domain

Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Computational approaches to investigating allostery

Conserved residue clustering and protein structure prediction.

Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface

Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server

Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

Druggable protein-protein interactions--from hot spots to hot segments.

Encounter complexes and dimensionality reduction in protein-protein association

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation

Evolving dual targeting of a prokaryotic protein in yeast.

Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins.

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility

Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals

Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family

FunHunt: model selection based on energy landscape characteristics.

Funnel hunting in a rough terrain: learning and discriminating native energy funnels.

Harnessing protein folding neural networks for peptide–protein docking

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.

Host FIH-Mediated Asparaginyl Hydroxylation of Translocated Legionella pneumophila Effectors

Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity

Identifying a common molecular mechanism for inhibition of MITF and STAT3 by PIAS3.

Improved side-chain modeling for protein-protein docking

In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2

Indirect ELISA-based approach for comparative measurement of high-affinity cohesin-dockerin interactions.

Is GAS1 a co-receptor for the GDNF family of ligands?

MYORG is associated with recessive primary familial brain calcification

Measurements of Relative Binding of Cohesin and Dockerin Mutants Using an Advanced ELISA Technique for High-Affinity Interactions

Minimizing and learning energy functions for side-chain prediction.

Mitochondrial complex IV deficiency, caused by mutated COX6B1, is associated with encephalomyopathy, hydrocephalus and cardiomyopathy

Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind

Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45

Modeling peptide-protein interactions

Molecular pathogenesis of human CD59 deficiency

Myelin-associated glycoprotein gene mutation causes Pelizaeus-Merzbacher disease-like disorder

Parkin Somatic Mutations Link Melanoma and Parkinson's Disease

Pathogens use structural mimicry of native host ligands as a mechanism for host receptor engagement

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how.

Peptiderive server: derive peptide inhibitors from protein-protein interactions

Phosphorylation of the WWOX Protein Regulates Its Interaction with p73

Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells

Progress in modeling of protein structures and interactions

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility

Protein-peptide docking: opportunities and challenges.

Protein-protein docking predictions for the CAPRI experiment

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

Rapid sampling of molecular motions with prior information constraints

Rationally Designed Macrocyclic Peptides as Synergistic Agonists of LPS-Induced Inflammatory Response

Relacin, a novel antibacterial agent targeting the Stringent Response

Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors

Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

RosettaDock in CAPRI rounds 6-12

Structural basis for UFM1 transfer from UBA5 to UFC1

Structure-Based Identification of HDAC8 Non-histone Substrates

Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates

Sub-angstrom modeling of complexes between flexible peptides and globular proteins.

The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK.

The SV40 capsid is stabilized by a conserved pentapeptide hinge of the major capsid protein VP1.

The structural basis of peptide-protein binding strategies.

The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite

Trans protein splicing of cyanobacterial split inteins in endogenous and exogenous combinations.

Ubiquitination and degradation of the inhibitors of NF-kappaB

Versatile communication strategies among tandem WW domain repeats

Yeast aconitase mitochondrial import is modulated by interactions of its C and N terminal domains and Ssa1/2 (Hsp70).

c-Abl phosphorylates E6AP and regulates its E3 ubiquitin ligase activity