Ruth Nussinov
Orcid: 0000-0002-8115-6415
According to our database1,
Ruth Nussinov
authored at least 115 papers
between 1982 and 2024.
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Bibliography
2024
Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics.
J. Chem. Inf. Model., 2024
2022
Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework.
Nat. Mac. Intell., November, 2022
HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry.
Bioinform., October, 2022
Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation.
J. Chem. Inf. Model., 2022
SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions.
Bioinform., 2022
2021
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization.
J. Chem. Inf. Model., 2021
Bioinform., 2021
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
2020
Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6, 700 cancer genomes.
PLoS Comput. Biol., 2020
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest.
Bioinform., 2020
2019
A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.
PLoS Comput. Biol., 2019
Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.
PLoS Comput. Biol., 2019
Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.
PLoS Comput. Biol., 2019
Bioinform., 2019
2017
2016
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.
PLoS Comput. Biol., 2016
PLoS Comput. Biol., 2016
Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation.
PLoS Comput. Biol., 2016
2015
Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics.
PLoS Comput. Biol., 2015
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.
PLoS Comput. Biol., 2015
Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization.
J. Chem. Inf. Model., 2015
Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein.
J. Comput. Biol., 2015
2014
The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer.
PLoS Comput. Biol., 2014
PLoS Comput. Biol., 2014
PLoS Comput. Biol., 2014
PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.
Nucleic Acids Res., 2014
2013
PLoS Comput. Biol., 2013
Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing.
J. Comput. Aided Mol. Des., 2013
2012
Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB.
PLoS Comput. Biol., 2012
A Strategy Based on Protein-Protein Interface Motifs May Help in Identifying Drug Off-Targets.
J. Chem. Inf. Model., 2012
Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review
CoRR, 2012
2011
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example.
PLoS Comput. Biol., 2011
A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides.
J. Comput. Chem., 2011
A Formal MIM Specification and Tools for the Common Exchange of MIM Diagrams: an XML-Based Format, an API, and a Validation Method.
BMC Bioinform., 2011
Bioinform., 2011
2010
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization.
PLoS Comput. Biol., 2010
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking.
Nucleic Acids Res., 2010
Nucleic Acids Res., 2010
2009
Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View.
PLoS Comput. Biol., 2009
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation.
PLoS Comput. Biol., 2009
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases.
Nucleic Acids Res., 2009
Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale.
J. Chem. Inf. Model., 2009
Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications.
J. Chem. Inf. Model., 2009
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces.
Briefings Bioinform., 2009
2008
Nucleic Acids Res., 2008
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions.
Nucleic Acids Res., 2008
Nucleic Acids Res., 2008
Nucleic Acids Res., 2008
Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design.
J. Chem. Inf. Model., 2008
Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules.
J. Comput. Biol., 2008
Bio-geometry: challenges, approaches, and future opportunities in proteomics and drug discovery.
Proceedings of the 2008 ACM Symposium on Solid and Physical Modeling, 2008
Proceedings of the Protein-protein Interactions and Networks: Identification, 2008
2007
EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps.
IEEE ACM Trans. Comput. Biol. Bioinform., 2007
PLoS Comput. Biol., 2007
2006
PLoS Comput. Biol., 2006
The Multiple Common Point Set Problem and Its Application to Molecule Binding Pattern Detection.
J. Comput. Biol., 2006
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.
Bioinform., 2006
2005
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces.
Nucleic Acids Res., 2005
Nucleic Acids Res., 2005
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005
Proceedings of the Research in Computational Molecular Biology, 2005
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005
Proceedings of the Computational Life Sciences, First International Symposium, 2005
2004
FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions.
J. Comput. Biol., 2004
Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004
2003
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003
2002
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002
2001
MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins.
J. Comput. Biol., 2001
A hierarchical, building-block-based computational scheme for protein structure prediction.
IBM J. Res. Dev., 2001
2000
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000
1999
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999
1998
A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility.
J. Comput. Biol., 1998
[Invited Lecture] Structural motifs in the interior and on the surfaces of protein monomers and at protein-protein interfaces.
Proceedings of the German Conference on Bioinformatics, 1998
1996
Proceedings of the Combinatorial Pattern Matching, 7th Annual Symposium, 1996
1995
An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching.
Comput. Appl. Biosci., 1995
1994
Proceedings of the 12th IAPR International Conference on Pattern Recognition, 1994
1993
Proceedings of the Combinatorial Pattern Matching, 4th Annual Symposium, 1993
1992
Proceedings of the Combinatorial Pattern Matching, Third Annual Symposium, 1992
1991
1989
RNA secondary structures: comparison and determination of frequently recurring substructures by consensus.
Comput. Appl. Biosci., 1989
1988
A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features.
Comput. Appl. Biosci., 1988
An improved secondary structure computation method and its application to intervening sequence in the human alpha-likeglobin mRNA precursors.
Comput. Appl. Biosci., 1988
Comput. Appl. Biosci., 1988
1986
Nucleic Acids Res., 1986
An efficient string matching algorithm with k differences for nucleotide and amino acid sequences.
Nucleic Acids Res., 1986
1984
An accelerated algorithm for calculating the secondary structure of single stranded RNAs.
Nucleic Acids Res., 1984
1982
Nucleic Acids Res., 1982
Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA.
Nucleic Acids Res., 1982