Shoshana J. Wodak

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Assessing the quality of macromolecular structures

Helen M. Berman, Shoshana J. Wodak, A. A. Vagin, 2006 .

Relating destabilizing regions to known functional sites in proteins

Shoshana J. Wodak, Benoit H. Dessailly, Marc F. Lensink, 2007, BMC Bioinformatics.

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

Shoshana J. Wodak, James Vlasblom, James Vlasblom, 2009, BMC Bioinformatics.

Representing and Analyzing Biochemical Networks Using BioMaze

Yves Deville, Shoshana J. Wodak, Christian Lemer, 2007 .

Generating and testing protein folds

Shoshana J. Wodak, Marianne Rooman, S. Wodak, 1993 .

Metabolic PathFinding: inferring relevant pathways in biochemical networks

Shoshana J. Wodak, Jacques van Helden, Didier Croes, 2005, Nucleic Acids Res..

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

Dario Strbenac, Mark D. Robinson, Shoshana J. Wodak, 2012, Nucleic Acids Res..

Detection of cavities in a set of interpenetrating spheres

Shoshana J. Wodak, Philippe Alard, S. Wodak, 1991 .

ACLAME: A CLAssification of Mobile genetic Elements

Shoshana J. Wodak, Raphaël Leplae, Aline Hebrant, 2004, Nucleic Acids Res..

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

Ian M. Donaldson, Andrei L. Turinsky, Shoshana J. Wodak, 2010, Database J. Biol. Databases Curation.

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

Shoshana J. Wodak, Thomas Simonson, Raul Mendez, 2007, BMC Bioinformatics.

Local coherence in genetic interaction patterns reveals prevalent functional versatility

Shoshana J. Wodak, James Vlasblom, Jack Greenblatt, 2008, Bioinform..

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

Shoshana J. Wodak, James Vlasblom, Shuye Pu, 2006, Bioinform..

Molecular Systematics in Three Dimensions

Shoshana J. Wodak, 1997, German Conference on Bioinformatics.

Coordination of structural bioinformatics activities across Europe

Sameer Velankar, Shoshana J. Wodak, Janet M. Thornton, 2018, Acta Crystallographica Section A: Foundations and Advances.

Faculty Opinions recommendation of Pi-Pi contacts are an overlooked protein feature relevant to phase separation.

Shoshana J. Wodak, 2019 .

Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data

Michael Schroeder, David R. Gilbert, Shoshana J. Wodak, 2000, JOBIM.

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

Yves Deville, Shoshana J. Wodak, Jean Richelle, 2004, Nucleic Acids Res..

Submit a Topic Page to PLOS Computational Biology and Wikipedia

Shoshana J. Wodak, Christophe Dessimoz, Daniel Mietchen, 2018, PLoS Comput. Biol..

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

Shoshana J. Wodak, Christine A. Orengo, Benoit H. Dessailly, 2007, Nucleic Acids Res..

Advanced pairwise structure alignments of proteins and analysis of conformational changes

Shoshana J. Wodak, Jean Richelle, Maria Elena Ochagavía, 2002, Bioinform..

Interactive computer animation of macromolecules

Shoshana J. Wodak, Philippe Delhaise, M. Bardiaux, 1984 .

Chapter 21.2 Assessing the quality of macromolecular structures

Helen M. Berman, Shoshana J. Wodak, A. A. Vagin, 2012 .

CYGD: the Comprehensive Yeast Genome Database

Shoshana J. Wodak, Christian Lemer, Jacques van Helden, 2004, Nucleic Acids Res..

Modeling protein assemblies: CAPRI 15 years hence 6th CAPRI evaluation meeting April 17‐19 Tel‐Aviv Israel

Shoshana J. Wodak, Joël Janin, 2016 .

Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, Cambridge, United Kingdom, July 16-19, 1995

Christopher J. Rawlings, Lawrence Hunter, Russ B. Altman, 1995, Intelligent Systems in Molecular Biology.

An Object-Oriented Data Model for Signal Transduction

Yves Deville, Shoshana J. Wodak, David Gilbert, 2003 .

Computer Graphics as an Aid in Protein Structure-Function Analysis and Design

Shoshana J. Wodak, S. Wodak, 1987 .

An overview of data models for the analysis of biochemical pathways

Yves Deville, David R. Gilbert, Shoshana J. Wodak, 2003, Briefings Bioinform..

Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database

David R. Gilbert, Shoshana J. Wodak, Kirill Degtyarenko, 1999, German Conference on Bioinformatics.

Predictions of Protein-Protein Interactions at the Atomic Scale

Shoshana J. Wodak, Marc F. Lensink, Raúl Méndez, 2007 .

State of the art in protein engineering and its application to enzymes and proteins in industry and agriculture

Shoshana J. Wodak, Marc Van Montagu, 1988 .

Développement d'outils théoriques et logiciels pour la modélisation du réseau des processus cellulaires

Shoshana J. Wodak, Vincent Devloo, 2003 .

Faculty Opinions recommendation of Protein structure determination using metagenome sequence data.

Shoshana J. Wodak, 2017 .

Computer aided design of macromolecules and A.I. approaches

Shoshana J. Wodak, Marianne Rooman, Bruno Marchal, 1986 .

Bioinformatics Applications Note Systems Biology Orthonets: Simultaneous Visual Analysis of Orthologs and Their Interaction Neighborhoods across Different Organisms

Andrei L. Turinsky, Shoshana J. Wodak, Andrei L. Turinsky, 2022 .

DAnCER: Disease-Annotated Chromatin Epigenetics Resource

Andrei L. Turinsky, Zhaolei Zhang, Shoshana J. Wodak, 2010, Nucleic Acids Res..

An Overview of Data Models for the Analysis of Biochemical Pathways

Yves Deville, David R. Gilbert, Shoshana J. Wodak, 2003, CMSB.

From Molecular Activities and Processes to Biological Function

Shoshana J. Wodak, Christian Lemer, Jacques van Helden, 2001, Briefings Bioinform..

Topic Pages: PLoS Computational Biology Meets Wikipedia

Robert B. Russell, Philip E. Bourne, Shoshana J. Wodak, 2012, PLoS Comput. Biol..

Macromolecular structure information and databases

Christopher J. Rawlings, Shoshana J. Wodak, Jean Richelle, 1996 .

BioEdge: a tool box for advanced analyses of biochemical networks

Yves Deville, Shoshana J. Wodak, Pierre Schaus, 2007 .

ISMB-95 -- Third international conference on intelligent systems for molecular biology: Proceedings

Christopher J. Rawlings, Lawrence Hunter, Thomas Lengauer, 1995 .

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

Ian M. Donaldson, Andrei L. Turinsky, Shoshana J. Wodak, 2010, Database J. Biol. Databases Curation.

Technical Approaches: Group Report

Shoshana J. Wodak, G. Winter, W. M. Barnes, 1986 .

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

Shoshana J. Wodak, Jacques van Helden, N. Simonis, 2004, Bioinform..

Review for "Assessment of domain interactions in CASP14"

Shoshana J. Wodak, 2021 .

Protein modules and protein-protein interaction

Shoshana J. Wodak, Joël Janin, J. Janin, 2003 .

Knowledge Based Potentials for Predicting the Three-Dimensional Conformation of Proteins

Shoshana J. Wodak, Jean-Pierre A. Kocher, Marianne Rooman, 1994 .

The TXP Motif in the Second Transmembrane Helix of CCR5

Shoshana J. Wodak, Marc Parmentier, Xavier Deupi, 2001, The Journal of Biological Chemistry.

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

Shoshana J. Wodak, S. Wodak, M. Rooman, 1988, Nature.

Location of structural domains in proteins

Shoshana J. Wodak, Joël Janin, J. Janin, 1981 .

Molecular dynamics simulation of polarizable water by an extended Lagrangian method

Shoshana J. Wodak, Matheus Froeyen, S. Wodak, 1992 .

Assessing Structural Predictions of Protein-Protein Recognition: The CAPRI Experiment

Sameer Velankar, Shoshana J. Wodak, Marc F. Lensink, 2015 .

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

Andrei L. Turinsky, Shoshana J. Wodak, James Vlasblom, 2015, Journal of proteomics.

Expanding the Landscape of Chromatin Modification (CM)-Related Functional Domains and Genes in Human

Andrei L. Turinsky, Zhaolei Zhang, Shoshana J. Wodak, 2010, PloS one.

Molecular dynamics study of methane hydration and methane association in a polarizable water phase

Shoshana J. Wodak, S. Wodak, D. V. Belle, 1993 .

Score_set: a CAPRI benchmark for Scoring protein complexes

Shoshana J. Wodak, Marc F. Lensink, 2014 .

Activation of CCR5 by Chemokines Involves an Aromatic Cluster between Transmembrane Helices 2 and 3*

Shoshana J. Wodak, Marc Parmentier, Leonardo Pardo, 2003, The Journal of Biological Chemistry.

Computer simulations of liquid water: treatment of long-range interactions

Shoshana J. Wodak, Martine Prévost, S. Wodak, 1990 .

Development and parametrization of continuum solvent models. I. Models based on the boundary element method

Shoshana J. Wodak, S. Wodak, G. Lippens, 1996 .

The brugel package - toward computer-aided-design of macromolecules

Shoshana J. Wodak, Philippe Alard, Martine Prévost, 1988 .

Extended Lagrangian formalism applied to temperature control and electronic polarization effects in molecular dynamics simulations

Shoshana J. Wodak, S. Wodak, D. V. Belle, 1995 .

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Chris Sander, Shoshana J. Wodak, Jean Richelle, 1998, Journal of molecular biology.

Identification of short turn motifs in proteins using sequence and structure fingerprints

Shoshana J. Wodak, Marianne Rooman, René Wintjens, 1994 .

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

Shoshana J. Wodak, Stephen S. MacKinnon, S. Wodak, 2015, Journal of molecular biology.