List of works by Shoshana Wodak

A benchmark testing ground for integrating homology modeling and protein docking

scientific article

A census of human soluble protein complexes

scientific article

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

scientific article published on 22 April 2020

A computer analysis of protein-protein interaction [proceedings]

scientific article published on May 1978

A conserved Asn in transmembrane helix 7 is an on/off switch in the activation of the thyrotropin receptor

scientific article

A structural domain of the covalent polymer globin chains of artemia. Interpretation of amino acid sequence data.

scientific article

ACLAME: a CLAssification of Mobile genetic Elements

scientific article

Activation of CCR5 by chemokines involves an aromatic cluster between transmembrane helices 2 and 3.

scientific article published on 30 October 2002

Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease

scientific article published in September 2011

Advanced pairwise structure alignments of proteins and analysis of conformational changes

scientific article

Allostery in Its Many Disguises: From Theory to Applications

scientific article published on 07 February 2019

Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power

scientific article

An Overview of Data Models for the Analysis of Biochemical Pathways

An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis

scientific article

An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis

An overview of data models for the analysis of biochemical pathways

scientific article

Analysis of zinc binding sites in protein crystal structures

scientific article published on August 1998

Analytical approximation to the accessible surface area of proteins.

scientific article

Are database-derived potentials valid for scoring both forward and inverted protein folding?

scientific article

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

scientific article

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation

scientific article published on 29 June 2015

Assessment of blind predictions of protein-protein interactions: current status of docking methods

scientific article

Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms

scientific article published in April 2011

Automatic analysis of protein conformational changes by multiple linkage clustering

scientific article

Automatic classification and analysis of alpha alpha-turn motifs in proteins

scientific article

Automatic definition of recurrent local structure motifs in proteins

scientific article published in May 1990

Automatic procedures for protein design

scientific article

Automatic protein design with all atom force-fields by exact and heuristic optimization

scientific article

Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition

scientific article

Basic design features of the parallel alpha beta barrel, a ubiquitous protein-folding motif

scientific article

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

scientific article

Blind predictions of protein interfaces by docking calculations in CAPRI ⬇️

scientific article published on November 15, 2010

Brain abnormalities in patients with Beckwith-Wiedemann syndrome.

scientific article

CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes

scientific article published in March 2024

CAPRI: a Critical Assessment of PRedicted Interactions

scientific article (publication date: July 2003)

CRYBA4, a novel human cataract gene, is also involved in microphthalmia

scientific article

CYGD: the Comprehensive Yeast Genome Database

scientific article

Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles

scientific article published in December 1987

Challenges and rewards of interaction proteomics

scientific article

Checking nucleic acid crystal structures

scientific article

Combining pattern discovery and discriminant analysis to predict gene co-regulation

article

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

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Complete therapeutic response of a large tubulovillous adenoma after chemotherapy.

scientific article published on 29 January 2017

Computational approaches to investigating allostery

scientific article published on 5 September 2016

Computational protein design is a challenge for implicit solvation models

scientific article published on 17 September 2004

Computational proteome-wide screening predicts neurotoxic drug-protein interactome for the investigational analgesic BIA 10-2474.

scientific article published on 19 December 2016

Computer analysis of protein-protein interaction

scientific article

Computer studies of interactions between macromolecules

scientific article

Computer-aided design in protein engineering

scientific article published in January 1987

Conformation of amino acid side-chains in proteins

scientific article

Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods

scientific article

Conformational properties of four peptides corresponding to alpha-helical regions of Rhodospirillum cytochrome c2 and bovine calcium binding protein

scientific article published on September 1994

Conserved water molecules in MHC class-I molecules and their putative structural and functional roles

scientific article

Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase

scientific article published on December 1991

Correction: Phenotypic Switching Induced by Damaged Matrix Is Associated with DNA Methyltransferase 3A (DNMT3A) Activity and Nuclear Localization in Smooth Muscle Cells (SMC).

scientific article published on 28 October 2013

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis

scientific article published in February 2008

Cover Image, Volume 85, Issue 3

scholarly article by Marc F. Lensink published in February 2017

Cover Image, Volume 88, Issue 8

DAnCER: disease-annotated chromatin epigenetics resource

scientific article

De novo missense variants in RAC3 cause a novel neurodevelopmental syndrome

Deviations from standard atomic volumes as a quality measure for protein crystal structures

scientific article

Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins

scientific article published on 20 May 2020

Docking and scoring protein complexes: CAPRI 3rd Edition

scientific article

Docking and scoring protein interactions: CAPRI 2009 ⬇️

scientific article published on November 15, 2010

Docking, scoring, and affinity prediction in CAPRI.

scientific article published on 17 October 2013

Editorial overview: Multi-protein assemblies in signaling

scientific article published on 23 November 2016

Effect of mutations within the peripheral anionic site on the stability of acetylcholinesterase

scientific article

Effect of nucleotide substrate binding on the pKa of catalytic residues in barnase

scientific article

Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human

scientific article

Extending molecular systematics to the third dimension

scientific article

Extracting high confidence protein interactions from affinity purification data: at the crossroads

scientific article

Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions

scientific article published on October 1992

Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins

scientific article published in October 1992

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches

scientific article

Folding free energy function selects native-like protein sequences in the core but not on the surface

scientific article

From molecular activities and processes to biological function

scientific article

From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent

scientific article

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks

scientific article published on September 2006

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways

scientific article

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

scientific article

Graph-based analysis of metabolic networks.

scientific article

Haemoglobin: the surface buried between the alpha 1 beta 1 and alpha 2 beta 2 dimers in the deoxy and oxy structures

scientific article published in May 1985

Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts

scientific article

High-throughput analyses and curation of protein interactions in yeast

scientific article published in January 2011

Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: Sequential assignment and secondary structure

scientific article (publication date: October 1993)

Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of histone H5

scientific article

Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation

scientific article

Identification of predictive sequence motifs limited by protein structure data base size

scientific article

Identification of structural domains in proteins by a graph heuristic

scientific article

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae

scientific article published on March 2007

Identifying structural domains in proteins.

scientific article

Inferring meaningful pathways in weighted metabolic networks

scientific article

Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators

Integration of Data from Liquid–Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers

Integrative bioinformatics: making sense of the networks

scientific article

Interaction databases on the same page

scientific article published in May 2011

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

scientific article

Intercellular network structure and regulatory motifs in the human hematopoietic system

scientific article

Interplay of buried histidine protonation and protein stability in prion misfolding

scientific article published on 13 April 2017

Interplay of self-association and conformational flexibility in regulating protein function

Intertwined associations in structures of homooligomeric proteins

scientific article published on 21 March 2013

Landscape of intertwined associations in multi-domain homo-oligomeric proteins

scientific article published on 11 November 2014

Lead generation and optimization based on protein-ligand complementarity.

scientific article published on 17 June 2010

LigASite--a database of biologically relevant binding sites in proteins with known apo-structures

scientific article published on 11 October 2007

Literature curation of protein interactions: measuring agreement across major public databases

scientific article

Local coherence in genetic interaction patterns reveals prevalent functional versatility

scientific article

Location of structural domains in protein

scientific article

Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium

scientific article published on July 1996

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs

scientific article

Mechanism and energy landscape of domain swapping in the B1 domain of protein G.

scientific article published on 17 June 2008

Metabolic PathFinding: inferring relevant pathways in biochemical networks

scientific article

Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats

scientific article

Modeling protein assemblies: Critical Assessment of Predicted Interactions (CAPRI) 15 years hence.: 6TH CAPRI evaluation meeting April 17-19 Tel-Aviv, Israel

scientific article published on 26 December 2016

Modeling protein interactions and complexes in CAPRI: Seventh CAPRI evaluation meeting, April 3-5 EMBL-EBI, Hinxton, UK

scientific article published on 19 February 2020

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

scientific article published on 16 November 2016

Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition

scientific article published on 30 December 2019

Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa

scientific article

Modelling the polypeptide backbone with 'spare parts' from known protein structures

scientific article

Modification of human hemoglobin by glutathione. III. Perturbations of hemoglobin conformation analyzed by computer modeling

scientific article published in November 1986

Modularity of the transcriptional response of protein complexes in yeast

scientific article published on 03 July 2006

Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C.

scientific article

Multiple replica repulsion technique for efficient conformational sampling of biological systems

scientific article

Mutations in chaperonin-like BBS genes are a major contributor to disease development in a multiethnic Bardet-Biedl syndrome patient population

scientific article published on 14 May 2010

NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels

scientific article

Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb

scientific article published on 01 January 2021

Navigating the global protein-protein interaction landscape using iRefWeb

scientific article published in January 2014

Next-generation protein engineering targets influenza

scientific article published on 7 June 2012

Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences

scientific article

Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins

scientific article

OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms

scientific article published on 20 January 2011

Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling.

scientific article published on May 2000

Pescador: the PEptides in Solution ConformAtion Database: Online Resource

scientific article

Phenotypic switching induced by damaged matrix is associated with DNA methyltransferase 3A (DNMT3A) activity and nuclear localization in smooth muscle cells (SMC)

scientific journal article

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

scientific article

Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions

scientific article

Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications

scientific article published on April 2004

Predictions of Protein-Protein Interactions at the Atomic Scale

Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins

scientific article

Properties of the protein matrix revealed by the free energy of cavity formation

scientific article

Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites

scientific article published on June 1992

Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 2. Site-directed mutagenesis of the xylose binding site

scientific article published on June 1992

Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 3. Changing metal specificity and the pH profile by site-directed mutagenesis

scientific article published in June 1992

Protein modules and protein-protein interaction. Introduction

scientific article

Protein structure prediction by threading methods: evaluation of current techniques

scientific article

Protein-protein interaction networks: the puzzling riches

scientific article

Reaction pathway for the quaternary structure change in hemoglobin

scientific article published in March 1985

Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets

scientific article

Recurrent alpha beta loop structures in TIM barrel motifs show a distinct pattern of conserved structural features.

scientific article

Relating destabilizing regions to known functional sites in proteins

scientific article

Relations between protein sequence and structure and their significance

scientific article published in May 1990

Representing and analysing molecular and cellular function using the computer

scientific article

Risk estimates for complex disorders: comparing personal genome testing and family history.

scientific article

Role of subunit interfaces in the allosteric mechanism of hemoglobin

scientific article

Role of the amino acid sequence in domain swapping of the B1 domain of protein G.

scientific article

SESAM: a relational database for structure and sequence of macromolecules.

scientific article

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

scientific article (publication date: 1999)

Savant Genome Browser 2: visualization and analysis for population-scale genomics

scientific article published on 25 May 2012

Score_set: a CAPRI benchmark for scoring protein complexes

scientific article published on 11 September 2014

Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase

scientific article

Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase

scientific article published in January 1991

Simulation of conformational changes in 2 Zn insulin

scientific article published in January 1985

Solution structure of the main alpha-amylase inhibitor from amaranth seeds

scientific article

Standard atomic volumes in double-stranded DNA and packing in protein--DNA interfaces

scientific article published on August 2001

Structural analysis of the 2.8 A model of Xylose isomerase from Actinoplanes missouriensis

scientific article

Structural basis of macromolecular recognition

scientific article

Structural biology: The transformational era

scientific article published in September 2023

Structural domains in proteins and their role in the dynamics of protein function

scientific article

Structural features of protein-nucleic acid recognition sites

scientific article

Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin

scientific article published in August 1990

Structural principles of parallel beta-barrels in proteins

scientific article

Submit a Topic Page to PLOS Computational Biology and Wikipedia

scientific article

The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity

scientific article published on 13 March 2019

The TXP motif in the second transmembrane helix of CCR5. A structural determinant of chemokine-induced activation

scientific article

The aMAZE LightBench: a web interface to a relational database of cellular processes

scientific article published on January 2004

The challenge of modeling protein assemblies: The CASP12-CAPRI experiment.

scientific article published on 10 November 2017

The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements.

scientific article

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses

scientific article

The quaternary structure of carbonmonoxy hemoglobin ypsilanti

scientific article published in January 1993

The structure of cytidilyl(2′,5′)adenosine when bound to pancreatic ribonuclease S ⬇️

scientific article published on November 1, 1977

The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007.

scientific article

Topic pages: PLoS Computational Biology meets Wikipedia

scientific article published in 2012

Transcriptional regulation of protein complexes in yeast

scientific article

Transfer nuclear Overhauser effect study of the conformation of oxytocin bound to bovine neurophysin I.

scientific article

Typical interaction patterns in alphabeta and betaalpha turn motifs

scientific article

Unfolding simulations of the 85-102 beta-hairpin of barnase

scientific article

Up-to-date catalogues of yeast protein complexes

scientific article published on 18 December 2008

Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins

scientific article published on January 1991

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

scientific article

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