List of works - Dina Schneidman-Duhovny

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

scientific article published on 18 August 2017

A method for integrative structure determination of protein-protein complexes

scientific article

Accurate SAXS profile computation and its assessment by contrast variation experiments

scientific article published on August 2013

An integrated suite of fast docking algorithms

scientific article

Approaching the CAPRI challenge with an efficient geometry-based docking

scientific article

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

scientific article

Automatic prediction of protein interactions with large scale motion

scientific article

Biallelic sequence variants in INTS1 in patients with developmental delays, cataracts, and craniofacial anomalies

scientific article published on 08 January 2019

Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness

scientific article published on 05 June 2020

BioInfo3D: a suite of tools for structural bioinformatics

scientific article published on July 2004

CRB2 mutations produce a phenotype resembling congenital nephrosis, Finnish type, with cerebral ventriculomegaly and raised alpha-fetoprotein

scientific article

CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2

scientific article published in 2024

Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer.

scientific article published on 26 September 2017

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

scientific article published on 4 February 2016

De novo STXBP1 mutation in a child with developmental delay and spasticity reveals a major structural alteration in the interface with syntaxin 1A

scientific article published on 19 August 2020

De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects.

scientific article published on 22 September 2017

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules

scientific article published on September 2008

DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1

scientific article

Dynamic Evolution of the Cthrc1 Genes, a Newly Defined Collagen-Like Family

scientific article published on 01 February 2020

Expansion of phenotype and genotypic data in CRB2-related syndrome

scientific article

FireDock: a web server for fast interaction refinement in molecular docking

scientific article published on 19 April 2008

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

scientific article published on 05 May 2016

FoXS: a web server for rapid computation and fitting of SAXS profiles

scientific article

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.

scientific article published on 31 January 2017

From structure to function: methods and applications

scientific article

Genetic interaction mapping informs integrative structure determination of protein complexes

scientific article published on 01 December 2020

Geometry-based flexible and symmetric protein docking

scientific article

HingeProt: automated prediction of hinges in protein structures

scientific article

Identification of the N-terminal peptide binding site of glucose-regulated protein 94.

scientific article

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

scientific article published on 12 October 2016

Integrative Structure Modeling: Overview and Assessment

scientific article published on 04 March 2019

Integrative structural modeling with small angle X-ray scattering profiles

scientific article

Integrative structure modeling of macromolecular assemblies from proteomics data

scientific article

Macromolecular docking restrained by a small angle X-ray scattering profile

scientific article

Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit

scientific article

Memdock: an α-helical membrane protein docking algorithm

scientific article published on 8 April 2016

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation

scientific article published on 19 September 2007

ModBase, a database of annotated comparative protein structure models and associated resources.

scientific article

ModBase, a database of annotated comparative protein structure models, and associated resources

scientific article

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles.

scientific article published in January 2018

Modeling of Multimolecular Complexes

scientific article published on 01 January 2020

Modeling of proteins and their assemblies with the Integrative Modeling Platform

scientific article published in January 2014

Modeling of proteins and their assemblies with the integrative modeling platform

scientific article published in January 2011

Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling

scientific article

Novel approach for efficient pharmacophore-based virtual screening: method and applications

scientific article published on October 2009

Optimized atomic statistical potentials: assessment of protein interfaces and loops

scientific article published on 27 September 2013

PatchDock and SymmDock: servers for rigid and symmetric docking

scientific article

PharmaGist: a webserver for ligand-based pharmacophore detection

scientific article published on 19 April 2008

Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition

scientific article published in PLoS ONE

Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking

scientific article published on January 2004

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering

scientific article

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

scientific article

Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages

scientific article

Recovering a representative conformational ensemble from underdetermined macromolecular structural data

scientific article

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes

scientific article published on 14 December 2013

Statistical potential for modeling and ranking of protein-ligand interactions

scientific article published on 21 November 2011

Structural Characterization of Full-Length Human Dehydrodolichyl Diphosphate Synthase Using an Integrative Computational and Experimental Approach

scientific article published on 28 October 2019

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

scientific article

Structural similarity of genetically interacting proteins

scientific article

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking

scientific article

The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor

scientific article published on 30 April 2020

The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor

scientific article (preprint)

The structural dynamics of macromolecular processes

scientific article published on 14 February 2009

UCSF Chimera, MODELLER, and IMP: an integrated modeling system

scientific article

Uncertainty in integrative structural modeling

scientific article

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

scientific article

Versatile, Multivalent Nanobody Cocktails Efficiently Neutralize SARS-CoV-2

scientific article published on 25 August 2020

List of works by Dina Schneidman-Duhovny

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

A method for integrative structure determination of protein-protein complexes

Accurate SAXS profile computation and its assessment by contrast variation experiments

An integrated suite of fast docking algorithms

Approaching the CAPRI challenge with an efficient geometry-based docking

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

Automatic prediction of protein interactions with large scale motion

Biallelic sequence variants in INTS1 in patients with developmental delays, cataracts, and craniofacial anomalies

Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness

BioInfo3D: a suite of tools for structural bioinformatics

CRB2 mutations produce a phenotype resembling congenital nephrosis, Finnish type, with cerebral ventriculomegaly and raised alpha-fetoprotein

CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2

Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer.

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

De novo STXBP1 mutation in a child with developmental delay and spasticity reveals a major structural alteration in the interface with syntaxin 1A

De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects.

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules

DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1

Dynamic Evolution of the Cthrc1 Genes, a Newly Defined Collagen-Like Family

Expansion of phenotype and genotypic data in CRB2-related syndrome

FireDock: a web server for fast interaction refinement in molecular docking

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

FoXS: a web server for rapid computation and fitting of SAXS profiles

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.

From structure to function: methods and applications

Genetic interaction mapping informs integrative structure determination of protein complexes

Geometry-based flexible and symmetric protein docking

HingeProt: automated prediction of hinges in protein structures

Identification of the N-terminal peptide binding site of glucose-regulated protein 94.

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

Integrative Structure Modeling: Overview and Assessment

Integrative structural modeling with small angle X-ray scattering profiles

Integrative structure modeling of macromolecular assemblies from proteomics data

Macromolecular docking restrained by a small angle X-ray scattering profile

Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit

Memdock: an α-helical membrane protein docking algorithm

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation

ModBase, a database of annotated comparative protein structure models and associated resources.

ModBase, a database of annotated comparative protein structure models, and associated resources

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles.

Modeling of Multimolecular Complexes

Modeling of proteins and their assemblies with the Integrative Modeling Platform

Modeling of proteins and their assemblies with the integrative modeling platform

Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling

Novel approach for efficient pharmacophore-based virtual screening: method and applications

Optimized atomic statistical potentials: assessment of protein interfaces and loops

PatchDock and SymmDock: servers for rigid and symmetric docking

PharmaGist: a webserver for ligand-based pharmacophore detection

Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition

Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages

Recovering a representative conformational ensemble from underdetermined macromolecular structural data

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes

Statistical potential for modeling and ranking of protein-ligand interactions

Structural Characterization of Full-Length Human Dehydrodolichyl Diphosphate Synthase Using an Integrative Computational and Experimental Approach

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

Structural similarity of genetically interacting proteins

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking

The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor

The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor

The structural dynamics of macromolecular processes

UCSF Chimera, MODELLER, and IMP: an integrated modeling system

Uncertainty in integrative structural modeling

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Versatile, Multivalent Nanobody Cocktails Efficiently Neutralize SARS-CoV-2