Ruth Nussinov

ORCID

Publication Activity (10 Years)

Years Active: 1982-2024
Publications (10 Years): 31

Top Venues

Publications

Nurit Haspel, Hyunbum Jang, Ruth Nussinov
Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics. J. Chem. Inf. Model. 64 (3) (2024)
Damla Ovek, Ameer Taweel, Zeynep Abali, Ece Tezsezen, Yunus Emre Koroglu, Chung-Jung Tsai, Ruth Nussinov, Ozlem Keskin, Attila Gürsoy
SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions. Bioinform. 38 (5) (2022)
Hao Zhang, Duan Ni, Jigang Fan, Minyu Li, Jian Zhang, Chen Hua, Ruth Nussinov, Shaoyong Lu
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. 62 (17) (2022)
Hansaim Lim, Chung-Jung Tsai, Ozlem Keskin, Ruth Nussinov, Attila Gürsoy
HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry. Bioinform. 38 (21) (2022)
Xiangxiang Zeng, Hongxin Xiang, Linhui Yu, Jianmin Wang, Kenli Li, Ruth Nussinov, Feixiong Cheng
Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework. Nat. Mac. Intell. 4 (11) (2022)
Xiaoqin Pan, Xuan Lin, Dongsheng Cao, Xiangxiang Zeng, Philip S. Yu, Lifang He, Ruth Nussinov, Feixiong Cheng
Deep learning for drug repurposing: methods, databases, and applications. CoRR (2022)
Tian Cai, Hansaim Lim, Kyra Alyssa Abbu, Yue Qiu, Ruth Nussinov, Lei Xie
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. J. Chem. Inf. Model. 61 (4) (2021)
Kazi Lutful Kabir, Ruth Nussinov, Buyong Ma, Amarda Shehu
Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics. BIBM (2021)
Chuang Liu, Zhen Han, Zi-Ke Zhang, Ruth Nussinov, Feixiong Cheng
A network-based deep learning methodology for stratification of tumor mutations. Bioinform. 37 (1) (2021)
Chuang Liu, Junfei Zhao, Weiqiang Lu, Yao Dai, Jennifer Hockings, Yadi Zhou, Ruth Nussinov, Charis Eng, Feixiong Cheng
Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6, 700 cancer genomes. PLoS Comput. Biol. 16 (2) (2020)
Xiangxiang Zeng, Siyi Zhu, Yuan Hou, Pengyue Zhang, Lang Li, Jing Li, L. Frank Huang, Stephen J. Lewis, Ruth Nussinov, Feixiong Cheng
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. Bioinform. 36 (9) (2020)
Ruth Nussinov, Chung-Jung Tsai, Hyunbum Jang
Protein ensembles link genotype to phenotype. PLoS Comput. Biol. 15 (6) (2019)
Xiangxiang Zeng, Siyi Zhu, Xiangrong Liu, Yadi Zhou, Ruth Nussinov, Feixiong Cheng
deepDR: a network-based deep learning approach to in silico drug repositioning. Bioinform. 35 (24) (2019)
Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng
Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput. Biol. 15 (3) (2019)
Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng
Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput. Biol. 15 (6) (2019)
He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng
A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications. PLoS Comput. Biol. 15 (2) (2019)
Emine Guven-Maiorov, Chung-Jung Tsai, Ruth Nussinov
Structural host-microbiota interaction networks. PLoS Comput. Biol. 13 (10) (2017)
Ruth Nussinov, Jason A. Papin, Ilya A. Vakser
Computing the Dynamic Supramolecular Structural Proteome. PLoS Comput. Biol. 13 (1) (2017)
Ruth Nussinov, Jason A. Papin
How can computation advance microbiome research? PLoS Comput. Biol. 13 (9) (2017)
Trey Ideker, Ruth Nussinov
Network approaches and applications in biology. PLoS Comput. Biol. 13 (10) (2017)
Ruth Nussinov, Jason A. Papin
Computing Biology. PLoS Comput. Biol. 12 (7) (2016)
Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput. Biol. 12 (4) (2016)
Rachel Karchin, Ruth Nussinov
Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation. PLoS Comput. Biol. 12 (8) (2016)
Jin Liu, Ruth Nussinov
Allostery: An Overview of Its History, Concepts, Methods, and Applications. PLoS Comput. Biol. 12 (6) (2016)
Liang Xu, Shengsheng Shan, Yonggang Chen, Xiaojuan Wang, Ruth Nussinov, Buyong Ma
Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization. J. Chem. Inf. Model. 55 (6) (2015)
Rudy Clausen, Buyong Ma, Ruth Nussinov, Amarda Shehu
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PLoS Comput. Biol. 11 (9) (2015)
Thomas Lengauer, Ruth Nussinov
How to Write a Presubmission Inquiry. PLoS Comput. Biol. 11 (2) (2015)
Ping Zhou, Ning Zhang, Ruth Nussinov, Buyong Ma
Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. J. Comput. Biol. 22 (9) (2015)
Ruth Nussinov, Sebastian Bonhoeffer, Jason A. Papin, Olaf Sporns
From "What Is?" to "What Isn't?" Computational Biology. PLoS Comput. Biol. 11 (7) (2015)
Amarda Shehu, Ruth Nussinov
Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics. PLoS Comput. Biol. 11 (10) (2015)
Ruth Nussinov
Advancements and Challenges in Computational Biology. PLoS Comput. Biol. 11 (1) (2015)
Alper Baspinar, Engin Cukuroglu, Ruth Nussinov, Ozlem Keskin, Attila Gürsoy
PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Qiang Cui, Ruth Nussinov
Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era. PLoS Comput. Biol. 10 (8) (2014)
Ruth Nussinov
The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead. PLoS Comput. Biol. 10 (1) (2014)
Chung-Jung Tsai, Ruth Nussinov
A Unified View of "How Allostery Works". PLoS Comput. Biol. 10 (2) (2014)
Shaoyong Lu, Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov, Jian Zhang
The Structural Basis of ATP as an Allosteric Modulator. PLoS Comput. Biol. 10 (9) (2014)
Mine Edes, Can C. Özturan, Türkan Haliloglu, Augustin Luna, Ruth Nussinov
MIMTool: A Tool for Drawing Molecular Interaction Maps. CoRR (2014)
Saliha Ece Acuner Ozbabacan, Attila Gürsoy, Ruth Nussinov, Ozlem Keskin
The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer. PLoS Comput. Biol. 10 (2) (2014)
Thomas Lengauer, Ruth Nussinov
. PLoS Comput. Biol. 9 (3) (2013)
David Zanuy, Francisco J. Sayago, Guillem Revilla-López, Gema Ballano, Lilach Agemy, Venkata Ramana Kotamraju, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, April M. Sawvel, Galen Stucky, Erkki Ruoslahti, Carlos Alemán
Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing. J. Comput. Aided Mol. Des. 27 (1) (2013)
Ruth Nussinov
Help the Biological Sciences? PLoS Comput. Biol. 9 (10) (2013)
Ruth Nussinov
. PLoS Comput. Biol. 8 (10) (2012)
Rosemary Dickin, Chris James Hall, Laura K. Taylor, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne
. PLoS Comput. Biol. 8 (1) (2012)
Elif Nihal Korkmaz, Ruth Nussinov, Türkan Haliloglu
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. 8 (3) (2012)
Billur Engin, Ozlem Keskin, Ruth Nussinov, Attila Gürsoy
A Strategy Based on Protein-Protein Interface Motifs May Help in Identifying Drug Off-Targets. J. Chem. Inf. Model. 52 (8) (2012)
Peter Csermely, Tamás Korcsmáros, Huba J. M. Kiss, Gabor London, Ruth Nussinov
Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review CoRR (2012)
David Curcó, David Zanuy, Ruth Nussinov, Carlos Alemán
A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides. J. Comput. Chem. 32 (4) (2011)
Ilona Kifer, Ruth Nussinov, Haim J. Wolfson
GOSSIP: a method for fast and accurate global alignment of protein structures. Bioinform. 27 (7) (2011)
Augustin Luna, Evrim I. Karac, Margot Sunshine, Lucas Chang, Ruth Nussinov, Mirit I. Aladjem, Kurt W. Kohn
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. 12 (2011)
Rosemary Dickin, Cecy Marden, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne
. PLoS Comput. Biol. 7 (1) (2011)
Yongping Pan, Ruth Nussinov
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example. PLoS Comput. Biol. 7 (6) (2011)
Guillem Revilla-López, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, Carlos Alemán, David Zanuy
Conformational Profile of a Proline-Arginine Hybrid. J. Chem. Inf. Model. 50 (10) (2010)
Yongping Pan, Ruth Nussinov
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization. PLoS Comput. Biol. 6 (8) (2010)
Shandar Ahmad, Ozlem Keskin, Kenji Mizuguchi, Akinori Sarai, Ruth Nussinov
CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Melda Tozluoglu, Ezgi Karaca, Ruth Nussinov, Türkan Haliloglu
A Mechanistic View of the Role of E3 in Sumoylation. PLoS Comput. Biol. 6 (8) (2010)
Nurcan Tuncbag, Gozde Kar, Ozlem Keskin, Attila Gürsoy, Ruth Nussinov
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Briefings Bioinform. 10 (3) (2009)
Yongping Pan, Ruth Nussinov
Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View. PLoS Comput. Biol. 5 (7) (2009)
David Zanuy, Gema Ballano, Ana I. Jiménez, Jordi Casanovas, Nurit Haspel, Carlos Cativiela, David Curcó, Ruth Nussinov, Carlos Alemán
Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale. J. Chem. Inf. Model. 49 (7) (2009)
Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases. Nucleic Acids Res. 37 (Database-Issue) (2009)
Oranit Dror, Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson
Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications. J. Chem. Inf. Model. 49 (10) (2009)
Jin Liu, Ruth Nussinov
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation. PLoS Comput. Biol. 5 (10) (2009)
Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson
Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules. J. Comput. Biol. 15 (7) (2008)
Ruth Nussinov, Tao Ju, Talapady Bhat, Jack Snoeyink, Karthik Ramani
Bio-geometry: challenges, approaches, and future opportunities in proteomics and drug discovery. Symposium on Solid and Physical Modeling (2008)
Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson
PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Francisco Rodríguez-Ropero, David Zanuy, Jordi Casanovas, Ruth Nussinov, Carlos Alemán
Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design. J. Chem. Inf. Model. 48 (2) (2008)
Efrat Mashiach, Dina Schneidman-Duhovny, Nelly Andrusier, Ruth Nussinov, Haim J. Wolfson
FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson, Roded Sharan
Structural similarity of genetically interacting proteins. BMC Syst. Biol. 2 (2008)
Eitan Yaffe, Dan Fishelovitch, Haim J. Wolfson, Dan Halperin, Ruth Nussinov
MolAxis: a server for identification of channels in macromolecules. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Zengjian Hu, Donnell Bowen, William M. Southerland, Antonio del Sol, Yongping Pan, Ruth Nussinov, Buyong Ma
Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR. PLoS Comput. Biol. 3 (6) (2007)
Yuval Inbar, Dina Schneidman-Duhovny, Oranit Dror, Ruth Nussinov, Haim J. Wolfson
Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules. RECOMB (2007)
Keren Lasker, Oranit Dror, Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Oranit Dror, Ruth Nussinov, Haim J. Wolfson
The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson
The Multiple Common Point Set Problem and Its Application to Molecule Binding Pattern Detection. J. Comput. Biol. 13 (2) (2006)
Gilad Wainreb, Nurit Haspel, Haim J. Wolfson, Ruth Nussinov
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly. Bioinform. 22 (11) (2006)
Chung-Jung Tsai, Jie Zheng, Ruth Nussinov
Designing a Nanotube Using Naturally Occurring Protein Building Blocks. PLoS Comput. Biol. 2 (4) (2006)
Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Oranit Dror, Ruth Nussinov, Haim J. Wolfson
ARTS: alignment of RNA tertiary structures. ECCB/JBI (2005)
Utkan Ogmen, Ozlem Keskin, A. Selim Aytuna, Ruth Nussinov, Attila Gürsoy
PRISM: protein interactions by structural matching. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Keren Lasker, Oranit Dror, Ruth Nussinov, Haim J. Wolfson
Discovery of Protein Substructures in EM Maps. WABI (2005)
Yuval Inbar, Haim J. Wolfson, Ruth Nussinov
Multiple Docking for Protein Structure Prediction. Int. J. Robotics Res. 24 (2-3) (2005)
Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
MAPPIS: Multiple 3D Alignment of Protein-Protein Interfaces. CompLife (2005)
Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson
PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson
Recognition of Binding Patterns Common to a Set of Protein Structures. RECOMB (2005)
Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions. J. Comput. Biol. 11 (1) (2004)
Alexandra Shulman-Peleg, Shira Mintz, Ruth Nussinov, Haim J. Wolfson
Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations. WABI (2004)
Maxim Shatsky, Oranit Dror, Dina Schneidman-Duhovny, Ruth Nussinov, Haim J. Wolfson
BioInfo3D: a suite of tools for structural bioinformatics. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Oranit Dror, Hadar Benyamini, Ruth Nussinov, Haim J. Wolfson
MASS: multiple structural alignment by secondary structures. ISMB (Supplement of Bioinformatics) (2003)
Yuval Inbar, Hadar Benyamini, Ruth Nussinov, Haim J. Wolfson
Protein structure prediction via combinatorial assembly of sub-structural units. ISMB (Supplement of Bioinformatics) (2003)
Dina Duhovny, Ruth Nussinov, Haim J. Wolfson
Efficient Unbound Docking of Rigid Molecules. WABI (2002)
Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
MultiProt - A Multiple Protein Structural Alignment Algorithm. WABI (2002)
Sandeep Kumar, Haim J. Wolfson, Ruth Nussinov
Protein flexibility and electrostatic interactions. IBM J. Res. Dev. 45 (3) (2001)
Nathaniel Leibowitz, Ruth Nussinov, Haim J. Wolfson
MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins. J. Comput. Biol. 8 (2) (2001)
Chung-Jung Tsai, Buyong Ma, Yuk Yin Sham, Sandeep Kumar, Haim J. Wolfson, Ruth Nussinov
A hierarchical, building-block-based computational scheme for protein structure prediction. IBM J. Res. Dev. 45 (3) (2001)
Maxim Shatsky, Zipora Y. Fligelman, Ruth Nussinov, Haim J. Wolfson
Alignment of Flexible Protein Structures. ISMB (2000)
Nathaniel Leibowitz, Zipora Y. Fligelman, Ruth Nussinov, Haim J. Wolfson
Multiple Structural Alignment and Core Detection by Geometric Hashing. ISMB (1999)
Bilha Sandak, Ruth Nussinov, Haim J. Wolfson
A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility. J. Comput. Biol. 5 (4) (1998)
Ruth Nussinov, Raquel Norel, Bilha Sandak, George Verbitsky, Haim J. Wolfson
[Invited Lecture] Structural motifs in the interior and on the surfaces of protein monomers and at protein-protein interfaces. German Conference on Bioinformatics (1998)
Bilha Sandak, Ruth Nussinov, Haim J. Wolfson
Docking of Conformationally Flexible Proteins. CPM (1996)

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Publication Activity (10 Years)

Top Topics

Top Venues

Ruth Nussinov