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Ruth Nussinov

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Concepts & Ideas

Chemicals & Drugs

Activities & Behaviors

Physiology

Protein Folding

Phenomena

Occupations

Genes & Molecular Sequences

Amino Acid Sequence

Procedures

Sequence Alignment

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Co-Publications
Name
97
Wolfson, Haim
62
Ma, Buyong
36
Tsai, Chung-Jung
25
Zanuy, David
20
Alemán, Carlos
15
Dror, Oranit
15
Haspel, Nurit
15
Shatsky, Maxim
14
Schneidman-Duhovny, Dina
11
Inbar, Yuval
11
Keskin, Ozlem
10
Cativiela, Carlos
10
Shulman-Peleg, Alexandra
9
Benyamini, Hadar
9
Casanovas, Jordi

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Publications

TOP 3
Pan Yongping; Tsai Chung-Jung; Ma Buyong; Nussinov Ruth
How do transcription factors select specific binding sites in the genome?
Boehr David D; Nussinov Ruth; Wright Peter E
The role of dynamic conformational ensembles in biomolecular recognition.
Mustata Mirela; Capone Ricardo; Jang Hyunbum; Arce Fernando Teran; Ramachandran Srinivasan; Lal Ratnesh; Nussinov Ruth
K3 fragment of amyloidogenic beta(2)-microglobulin forms ion channels: implication for dialysis related amyloidosis.

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All Publications

2009: Pan Yongping; Tsai Chung-Jung; Ma Buyong; Nussinov Ruth
How do transcription factors select specific binding sites in the genome?
Nature structural & molecular biology 2009;16(11):1118-20.
2009: Boehr David D; Nussinov Ruth; Wright Peter E
The role of dynamic conformational ensembles in biomolecular recognition.
Nature chemical biology 2009;5(11):789-96.
2009: Mustata Mirela; Capone Ricardo; Jang Hyunbum; Arce Fernando Teran; Ramachandran Srinivasan; Lal Ratnesh; Nussinov Ruth
K3 fragment of amyloidogenic beta(2)-microglobulin forms ion channels: implication for dialysis related amyloidosis.
Journal of the American Chemical Society 2009;131(41):14938-45.
2009: Dror Oranit; Schneidman-Duhovny Dina; Inbar Yuval; Nussinov Ruth; Wolfson Haim J
Novel approach for efficient pharmacophore-based virtual screening: method and applications.
Journal of chemical information and modeling 2009;49(10):2333-43.
2009: Liu Jin; Nussinov Ruth
The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation.
PLoS computational biology 2009;5(10):e1000527.
2009: Alemán Carlos; Jiménez Ana I; Cativiela Carlos; Nussinov Ruth; Casanovas Jordi
Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue.
The Journal of organic chemistry 2009;74(20):7834-43.
2009: Fishelovitch Dan; Shaik Sason; Wolfson Haim J; Nussinov Ruth
Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism.
The journal of physical chemistry. B 2009;113(39):13018-25.
2009: Miller Yifat; Ma Buyong; Nussinov Ruth
Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation.
Biophysical journal 2009;97(4):1168-77.
2009: del Sol Antonio; Tsai Chung-Jung; Ma Buyong; Nussinov Ruth
The origin of allosteric functional modulation: multiple pre-existing pathways.
Structure (London, England : 1993) 2009;17(8):1042-50.
2009: Pan Yongping; Nussinov Ruth
Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.
PLoS computational biology 2009;5(7):e1000448.
2009: Zanuy David; Ballano Gema; Jiménez Ana I; Casanovas Jordi; Haspel Nurit; Cativiela Carlos; Curcó David; Nussinov Ruth; Alemán Carlos
Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale.
Journal of chemical information and modeling 2009;49(7):1623-9.
2009: Zanuy David; Flores-Ortega Alejandra; Jiménez Ana I; Calaza M Isabel; Cativiela Carlos; Nussinov Ruth; Ruoslahti Erkki; Alemán Carlos
In silico molecular engineering for a targeted replacement in a tumor-homing peptide.
The journal of physical chemistry. B 2009;113(22):7879-89.
2009: Tuncbag Nurcan; Kar Gozde; Keskin Ozlem; Gursoy Attila; Nussinov Ruth
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces.
Briefings in bioinformatics 2009;10(3):217-32.
2009: Ma Buyong; Nussinov Ruth
Amplification of signaling via cellular allosteric relay and protein disorder.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(17):6887-8.
2009: Carbonell Pablo; Nussinov Ruth; del Sol Antonio
Energetic determinants of protein binding specificity: insights into protein interaction networks.
Proteomics 2009;9(7):1744-53.
2009: Revilla-López Guillem; Torras Juan; Jiménez Ana I; Cativiela Carlos; Nussinov Ruth; Alemán Carlos
Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue.
The Journal of organic chemistry 2009;74(6):2403-12.
2009: Tsai Chung-Jung; Del Sol Antonio; Nussinov Ruth
Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms.
Molecular bioSystems 2009;5(3):207-16.
2009: Buch Idit; Brooks Bernard R; Wolfson Haim J; Nussinov Ruth
Computational validation of protein nanotubes.
Nano letters 2009;9(3):1096-102.
2009: Yu Xiang; Wang Qiuming; Yang Jui-Chen; Buch Idit; Tsai Chung-Jung; Ma Buyong; Cheng Stephen Z D; Nussinov Ruth; Zheng Jie
Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain.
Biomacromolecules 2009;10(2):390-9.
2009: Ma Buyong; Nussinov Ruth
Regulating highly dynamic unstructured proteins and their coding mRNAs.
Genome biology 2009;10(1):204.
2009: Pappu Rohit V; Nussinov Ruth
Protein folding: lessons learned and new frontiers. Preface.
Physical biology 2009;6(1):10301.
2009: Tsai Chung-Jung; Ma Buyong; Nussinov Ruth
Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control.
Physical biology 2009;6(1):13001.
2009: Zanuy David; Curcó David; Nussinov Ruth; Alemán Carlos
Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptide.
Biopolymers 2009;92(2):83-93.
2008: Gursoy Attila; Keskin Ozlem; Nussinov Ruth
Topological properties of protein interaction networks from a structural perspective.
Biochemical Society transactions 2008;36(Pt 6):1398-403.
2008: Flores-Ortega Alejandra; Casanovas Jordi; Nussinov Ruth; Alemán Carlos
Conformational preferences of beta- and gamma-aminated proline analogues.
The journal of physical chemistry. B 2008;112(44):14045-55.
2008: Abraham Mira; Dror Oranit; Nussinov Ruth; Wolfson Haim J
Analysis and classification of RNA tertiary structures.
RNA (New York, N.Y.) 2008;14(11):2274-89.
2008: Tsai Chung-Jung; Sauna Zuben E; Kimchi-Sarfaty Chava; Ambudkar Suresh V; Gottesman Michael M; Nussinov Ruth
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima.
Journal of molecular biology 2008;383(2):281-91.
2008: Jang Hyunbum; Ma Buyong; Lal Ratnesh; Nussinov Ruth
Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels.
Biophysical journal 2008;95(10):4631-42.
2008: Andrusier Nelly; Mashiach Efrat; Nussinov Ruth; Wolfson Haim J
Principles of flexible protein-protein docking.
Proteins 2008;73(2):271-89.
2008: Kifer Ilona; Nussinov Ruth; Wolfson Haim J
Constructing templates for protein structure prediction by simulation of protein folding pathways.
Proteins 2008;73(2):380-94.
2008: Ballano Gema; Zanuy David; Jiménez Ana I; Cativiela Carlos; Nussinov Ruth; Alemán Carlos
Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids.
The journal of physical chemistry. B 2008;112(41):13101-15.
2008: Ahmad Shandar; Keskin Ozlem; Sarai Akinori; Nussinov Ruth
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.
Nucleic acids research 2008;36(18):5922-32.
2008: Yaffe Eitan; Fishelovitch Dan; Wolfson Haim J; Halperin Dan; Nussinov Ruth
MolAxis: efficient and accurate identification of channels in macromolecules.
Proteins 2008;73(1):72-86.
2008: Schneidman-Duhovny Dina; Dror Oranit; Inbar Yuval; Nussinov Ruth; Wolfson Haim J
Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(7):737-54.
2008: Tozluoglu Melda; Karaca Ezgi; Haliloglu Turkan; Nussinov Ruth
Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis.
Nucleic acids research 2008;36(15):5033-49.
2008: Tuncbag Nurcan; Gursoy Attila; Guney Emre; Nussinov Ruth; Keskin Ozlem
Architectures and functional coverage of protein-protein interfaces.
Journal of molecular biology 2008;381(3):785-802.
2008: Zanuy David; Flores-Ortega Alejandra; Casanovas Jordi; Curcó David; Nussinov Ruth; Alemán Carlos
The energy landscape of a selective tumor-homing pentapeptide.
The journal of physical chemistry. B 2008;112(29):8692-700.
2008: Shulman-Peleg Alexandra; Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions.
Nucleic acids research 2008;36(Web Server issue):W260-4.
2008: Yaffe Eitan; Fishelovitch Dan; Wolfson Haim J; Halperin Dan; Nussinov Ruth
MolAxis: a server for identification of channels in macromolecules.
Nucleic acids research 2008;36(Web Server issue):W210-5.
2008: Schneidman-Duhovny Dina; Dror Oranit; Inbar Yuval; Nussinov Ruth; Wolfson Haim J
PharmaGist: a webserver for ligand-based pharmacophore detection.
Nucleic acids research 2008;36(Web Server issue):W223-8.
2008: Mashiach Efrat; Schneidman-Duhovny Dina; Andrusier Nelly; Nussinov Ruth; Wolfson Haim J
FireDock: a web server for fast interaction refinement in molecular docking.
Nucleic acids research 2008;36(Web Server issue):W229-32.
2008: Casanovas Jordi; Nussinov Ruth; Alemán Carlos
Intrinsic conformational preferences of C(alpha,alpha)-dibenzylglycine.
The Journal of organic chemistry 2008;73(11):4205-11.
2008: Zheng Jie; Jang Hyunbum; Ma Buyong; Nussinov Ruth
Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42.
The journal of physical chemistry. B 2008;112(22):6856-65.
2008: Pan Yongping; Nussinov Ruth
p53-Induced DNA bending: the interplay between p53-DNA and p53-p53 interactions.
The journal of physical chemistry. B 2008;112(21):6716-24.
2008: Shulman-Peleg Alexandra; Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
Prediction of interacting single-stranded RNA bases by protein-binding patterns.
Journal of molecular biology 2008;379(2):299-316.
2008: Flores-Ortega Alejandra; Jiménez Ana I; Cativiela Carlos; Nussinov Ruth; Alemán Carlos; Casanovas Jordi
Conformational preferences of alpha-substituted proline analogues.
The Journal of organic chemistry 2008;73(9):3418-27.
2008: Yogurtcu Osman N; Erdemli S Bora; Nussinov Ruth; Turkay Metin; Keskin Ozlem
Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations.
Biophysical journal 2008;94(9):3475-85.
2008: Keskin Ozlem; Gursoy Attila; Ma Buyong; Nussinov Ruth
Principles of protein-protein interactions: what are the preferred ways for proteins to interact?
Chemical reviews 2008;108(4):1225-44.
2008: Tsai Chung-Jung; del Sol Antonio; Nussinov Ruth
Allostery: absence of a change in shape does not imply that allostery is not at play.
Journal of molecular biology 2008;378(1):1-11.
2008: Emekli Ugur; Schneidman-Duhovny Dina; Wolfson Haim J; Nussinov Ruth; Haliloglu Turkan
HingeProt: automated prediction of hinges in protein structures.
Proteins 2008;70(4):1219-27.
2008: Zheng Jie; Jang Hyunbum; Nussinov Ruth
Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific.
Biochemistry 2008;47(8):2497-509.
2008: Rodríguez-Ropero Francisco; Zanuy David; Casanovas Jordi; Nussinov Ruth; Alemán Carlos
Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design.
Journal of chemical information and modeling 2008;48(2):333-43.
2008: Jang Hyunbum; Zheng Jie; Lal Ratnesh; Nussinov Ruth
New structures help the modeling of toxic amyloidbeta ion channels.
Trends in biochemical sciences 2008;33(2):91-100.
2008: Liu Jin; Nussinov Ruth
Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(3):901-6.
2008: Casanovas Jordi; Jiménez Ana I; Cativiela Carlos; Nussinov Ruth; Alemán Carlos
1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue.
The Journal of organic chemistry 2008;73(2):644-51.
2008: Gazit Ehud; Nussinov Ruth
Nanostructure design: methods and protocols. Preface.
Methods in molecular biology (Clifton, N.J.) 2008;474():v-vii.
2008: Emekli Ugur; Gunasekaran K; Nussinov Ruth; Haliloglu Turkan
What can we learn from highly connected beta-rich structures for structural interface design?
Methods in molecular biology (Clifton, N.J.) 2008;474():235-53.
2008: Buch Idit; Tsai Chung-Jung; Wolfson Haim J; Nussinov Ruth
Self-assembly of fused homo-oligomers to create nanotubes.
Methods in molecular biology (Clifton, N.J.) 2008;474():117-31.
2008: Dror Oranit; Schneidman-Duhovny Dina; Shulman-Peleg Alexandra; Nussinov Ruth; Wolfson Haim J; Sharan Roded
Structural similarity of genetically interacting proteins.
BMC systems biology 2008;2():69.
2008: Keskin Ozlem; Nussinov Ruth; Gursoy Attila
PRISM: protein-protein interaction prediction by structural matching.
Methods in molecular biology (Clifton, N.J.) 2008;484():505-21.
2008: Zheng Jie; Ma Buyong; Chang Yung; Nussinov Ruth
Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association.
Frontiers in bioscience : a journal and virtual library 2008;13():3919-30.
2008: Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.
Methods in molecular biology (Clifton, N.J.) 2008;413():125-46.
2007: Curcó David; Nussinov Ruth; Alemán Carlos
Coarse-graining the self-assembly of beta-helical protein building blocks.
The journal of physical chemistry. B 2007;111(50):14006-11.
2007: Fishelovitch Dan; Hazan Carina; Hirao Hajime; Wolfson Haim J; Nussinov Ruth; Shaik Sason
QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding.
The journal of physical chemistry. B 2007;111(49):13822-32.
2007: Schneidman-Duhovny Dina; Nussinov Ruth; Wolfson Haim J
Automatic prediction of protein interactions with large scale motion.
Proteins 2007;69(4):764-73.
2007: Zanuy David; Rodríguez-Ropero Francisco; Nussinov Ruth; Alemán Carlos
Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics study.
Journal of structural biology 2007;160(2):177-89.
2007: Zheng Jie; Jang Hyunbum; Ma Buyong; Tsai Chung-Jun; Nussinov Ruth
Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.
Biophysical journal 2007;93(9):3046-57.
2007: Zanuy David; Rodríguez-Ropero Francisco; Haspel Nurit; Zheng Jie; Nussinov Ruth; Aleman Carlos
Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences.
Biomacromolecules 2007;8(10):3135-46.
2007: Andrusier Nelly; Nussinov Ruth; Wolfson Haim J
FireDock: fast interaction refinement in molecular docking.
Proteins 2007;69(1):139-59.
2007: Curcó David; Nussinov Ruth; Aleman Carlos
Coarse-grained representation of beta-helical protein building blocks.
The journal of physical chemistry. B 2007;111(35):10538-49.
2007: Jang Hyunbum; Zheng Jie; Nussinov Ruth
Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process.
Biophysical journal 2007;93(6):1938-49.
2007: Haspel Nurit; Zanuy David; Zheng Jie; Aleman Carlos; Wolfson Haim; Nussinov Ruth
Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer.
Biophysical journal 2007;93(1):245-53.
2007: Tsai Chung-Jung; Zheng Jie; Zanuy David; Haspel Nurit; Wolfson Haim; Alemán Carlos; Nussinov Ruth
Principles of nanostructure design with protein building blocks.
Proteins 2007;68(1):1-12.
2007: Hu Zengjian; Bowen Donnell; Southerland William M; del Sol Antonio; Pan Yongping; Nussinov Ruth; Ma Buyong
Ligand binding and circular permutation modify residue interaction network in DHFR.
PLoS computational biology 2007;3(6):e117.
2007: Flores-Ortega Alejandra; Casanovas Jordi; Zanuy David; Nussinov Ruth; Alemán Carlos
Conformations of proline analogues having double bonds in the ring.
The journal of physical chemistry. B 2007;111(19):5475-82.
2007: Zanuy David; Jiménez Ana I; Cativiela Carlos; Nussinov Ruth; Alemán Carlos
Use of constrained synthetic amino acids in beta-helix proteins for conformational control.
The journal of physical chemistry. B 2007;111(12):3236-42.
2007: Keskin Ozlem; Nussinov Ruth
Similar binding sites and different partners: implications to shared proteins in cellular pathways.
Structure (London, England : 1993) 2007;15(3):341-54.
2007: Casanovas Jordi; Zanuy David; Nussinov Ruth; Alemán Carlos
Intrinsic conformational characteristics of alpha,alpha-diphenylglycine.
The Journal of organic chemistry 2007;72(6):2174-81.
2007: Fishelovitch Dan; Hazan Carina; Shaik Sason; Wolfson Haim J; Nussinov Ruth
Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4.
Journal of the American Chemical Society 2007;129(6):1602-11.
2007: Zheng Jie; Zanuy David; Haspel Nurit; Tsai Chung-Jung; Alemán Carlos; Nussinov Ruth
Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues.
Biochemistry 2007;46(5):1205-18.
2007: Lasker Keren; Dror Oranit; Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2007;4(1):28-39.
2007: Dror Oranit; Lasker Keren; Nussinov Ruth; Wolfson Haim
EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 1):42-9.
2007: Pan Yongping; Nussinov Ruth
Structural basis for p53 binding-induced DNA bending.
The Journal of biological chemistry 2007;282(1):691-9.
2007: Gunasekaran Kannan; Nussinov Ruth
How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding.
Journal of molecular biology 2007;365(1):257-73.
2007: Shulman-Peleg Alexandra; Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
Spatial chemical conservation of hot spot interactions in protein-protein complexes.
BMC biology 2007;5():43.
2007: Cohen-Gihon Inbar; Nussinov Ruth; Sharan Roded
Comprehensive analysis of co-occurring domain sets in yeast proteins.
BMC genomics 2007;8():161.
2007: Del Sol Antonio; Araúzo-Bravo Marcos J; Amoros Dolors; Nussinov Ruth
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages.
Genome biology 2007;8(5):R92.
2007: Ma Buyong; Nussinov Ruth
Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design.
Current topics in medicinal chemistry 2007;7(10):999-1005.
2007: Keskin O; Gursoy A; Ma B; Nussinov R
Towards drugs targeting multiple proteins in a systems biology approach.
Current topics in medicinal chemistry 2007;7(10):943-51.
2007: Ma Buyong; Pan Yongping; Zheng Jie; Levine Arnold J; Nussinov Ruth
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.
Nucleic acids research 2007;35(9):2986-3001.
2007: Jang Hyunbum; Ma Buyong; Nussinov Ruth
Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect.
BMC structural biology 2007;7():21.
2007: Haspel Nurit; Wainreb Gilad; Inbar Yuval; Tsai Hui-Hsu; Tsai Chung-Jung; Wolfson Haim J; Nussinov Ruth
A hierarchical protein folding scheme based on the building block folding model.
Methods in molecular biology (Clifton, N.J.) 2007;350():189-204.
2006: Liu Jin; Pan Yongping; Ma Buyong; Nussinov Ruth
"Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains.
Structure (London, England : 1993) 2006;14(12):1811-21.
2006: Aleman Carlos; Zanuy David; Casanovas Jordi; Cativiela Carlos; Nussinov Ruth
Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid.
The journal of physical chemistry. B 2006;110(42):21264-71.
2006: Ertekin Asli; Nussinov Ruth; Haliloglu Turkan
Association of putative concave protein-binding sites with the fluctuation behavior of residues.
Protein science : a publication of the Protein Society 2006;15(10):2265-77.
2006: Ma Buyong; Nussinov Ruth
Simulations as analytical tools to understand protein aggregation and predict amyloid conformation.
Current opinion in chemical biology 2006;10(5):445-52.
2006: Tsai Chung-Jung; Zheng Jie; Alemán Carlos; Nussinov Ruth
Structure by design: from single proteins and their building blocks to nanostructures.
Trends in biotechnology 2006;24(10):449-54.
2006: Jang Hyunbum; Ma Buyong; Woolf Thomas B; Nussinov Ruth
Interaction of protegrin-1 with lipid bilayers: membrane thinning effect.
Biophysical journal 2006;91(8):2848-59.
2006: Zheng Jie; Ma Buyong; Nussinov Ruth
Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure.
Physical biology 2006;3(3):P1-4.
2006: del Sol Antonio; Fujihashi Hirotomo; Amoros Dolors; Nussinov Ruth
Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families.
Protein science : a publication of the Protein Society 2006;15(9):2120-8.
2006: Zheng Jie; Ma Buyong; Tsai Chung-Jung; Nussinov Ruth
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
Biophysical journal 2006;91(3):824-33.
2006: Dror Oranit; Nussinov Ruth; Wolfson Haim J
The ARTS web server for aligning RNA tertiary structures.
Nucleic acids research 2006;34(Web Server issue):W412-5.
2006: Haspel Nurit; Zanuy David; Alemán Carlos; Wolfson Haim; Nussinov Ruth
De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs.
Structure (London, England : 1993) 2006;14(7):1137-48.
2006: Tsai Hui-Hsu Gavin; Gunasekaran Kannan; Nussinov Ruth
Sequence and structure analysis of parallel beta helices: implication for constructing amyloid structural models.
Structure (London, England : 1993) 2006;14(6):1059-72.
2006: Wainreb Gilad; Haspel Nurit; Wolfson Haim J; Nussinov Ruth
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.
Bioinformatics (Oxford, England) 2006;22(11):1343-52.
2006: Halperin Inbal; Wolfson Haim; Nussinov Ruth
Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families.
Proteins 2006;63(4):832-45.
2006: Ma Buyong; Nussinov Ruth
The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.
Biophysical journal 2006;90(10):3365-74.
2006: Tsai Chung-Jung; Zheng Jie; Nussinov Ruth
Designing a nanotube using naturally occurring protein building blocks.
PLoS computational biology 2006;2(4):e42.
2006: Zanuy David; Gunasekaran Kannan; Lesk Arthur M; Nussinov Ruth
Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.
Journal of molecular biology 2006;358(1):330-45.
2006: Shatsky Maxim; Shulman-Peleg Alexandra; Nussinov Ruth; Wolfson Haim J
The multiple common point set problem and its application to molecule binding pattern detection.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(2):407-28.
2006: Zanuy David; Nussinov Ruth; Alemán Carlos
From peptide-based material science to protein fibrils: discipline convergence in nanobiology.
Physical biology 2006;3(1):S80-90.
2006: Alemán Carlos; Zanuy David; Jiménez Ana I; Cativiela Carlos; Haspel Nurit; Zheng Jie; Casanovas Jordi; Wolfson Haim; Nussinov Ruth
Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids.
Physical biology 2006;3(1):S54-62.
2006: Pan Yongping; Ma Buyong; Levine Arnold J; Nussinov Ruth
Comparison of the human and worm p53 structures suggests a way for enhancing stability.
Biochemistry 2006;45(12):3925-33.
2006: Gnanakaran S; Nussinov Ruth; García Angel E
Atomic-level description of amyloid beta-dimer formation.
Journal of the American Chemical Society 2006;128(7):2158-9.
2006: Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
Optimization of multiple-sequence alignment based on multiple-structure alignment.
Proteins 2006;62(1):209-17.
2006: del Sol Antonio; Fujihashi Hirotomo; Amoros Dolors; Nussinov Ruth
Residues crucial for maintaining short paths in network communication mediate signaling in proteins.
Molecular systems biology 2006;2():2006.0019.
2006: Shaul Shaul; Nussinov Ruth; Pupko Tal
Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms.
BMC evolutionary biology 2006;6():22.
2005: Inbar Yuval; Benyamini Hadar; Nussinov Ruth; Wolfson Haim J
Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies.
Physical biology 2005;2(4):S156-65.
2005: Benyamini Hadar; Gunasekaran Kannan; Wolfson Haim; Nussinov Ruth
Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis.
Biochimica et biophysica acta 2005;1753(1):121-30.
2005: Mintz Shira; Shulman-Peleg Alexandra; Wolfson Haim J; Nussinov Ruth
Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions.
Proteins 2005;61(1):6-20.
2005: Dror Oranit; Nussinov Ruth; Wolfson Haim
ARTS: alignment of RNA tertiary structures.
Bioinformatics (Oxford, England) 2005;21 Suppl 2():ii47-53.
2005: Tsai Chung-Jung; Nussinov Ruth
The implications of higher (or lower) success in secondary structure prediction of chain fragments.
Protein science : a publication of the Protein Society 2005;14(8):1943-4.
2005: Schneidman-Duhovny Dina; Inbar Yuval; Nussinov Ruth; Wolfson Haim J
Geometry-based flexible and symmetric protein docking.
Proteins 2005;60(2):224-31.
2005: Inbar Yuval; Schneidman-Duhovny Dina; Halperin Inbal; Oron Assaf; Nussinov Ruth; Wolfson Haim J
Approaching the CAPRI challenge with an efficient geometry-based docking.
Proteins 2005;60(2):217-23.
2005: Ogmen Utkan; Keskin Ozlem; Aytuna A Selim; Nussinov Ruth; Gursoy Attila
PRISM: protein interactions by structural matching.
Nucleic acids research 2005;33(Web Server issue):W331-6.
2005: Schneidman-Duhovny Dina; Inbar Yuval; Nussinov Ruth; Wolfson Haim J
PatchDock and SymmDock: servers for rigid and symmetric docking.
Nucleic acids research 2005;33(Web Server issue):W363-7.
2005: Shulman-Peleg Alexandra; Nussinov Ruth; Wolfson Haim J
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces.
Nucleic acids research 2005;33(Web Server issue):W337-41.
2005: Pan Yongping; Ma Buyong; Nussinov Ruth
CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible.
Journal of molecular biology 2005;350(3):514-27.
2005: Ma Buyong; Pan Yongping; Gunasekaran K; Keskin Ozlem; Venkataraghavan R Babu; Levine Arnold J; Nussinov Ruth
The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins.
Physical biology 2005;2(2):S56-66.
2005: Keskin Ozlem; Ma Buyong; Rogale Kristina; Gunasekaran K; Nussinov Ruth
Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach.
Physical biology 2005;2(2):S24-35.
2005: Tsai Hui-Hsu Gavin; Reches Meital; Tsai Chung-Jung; Gunasekaran Kannan; Gazit Ehud; Nussinov Ruth
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(23):8174-9.
2005: Inbar Yuval; Benyamini Hadar; Nussinov Ruth; Wolfson Haim J
Prediction of multimolecular assemblies by multiple docking.
Journal of molecular biology 2005;349(2):435-47.
2005: Wolfson Haim J; Shatsky Maxim; Schneidman-Duhovny Dina; Dror Oranit; Shulman-Peleg Alexandra; Ma Buyong; Nussinov Ruth
From structure to function: methods and applications.
Current protein & peptide science 2005;6(2):171-83.
2005: Ma Buyong; Pan Yongping; Gunasekaran K; Venkataraghavan R Babu; Levine Arnold J; Nussinov Ruth
Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(11):3988-93.
2005: Haliloglu Turkan; Keskin Ozlem; Ma Buyong; Nussinov Ruth
How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
Biophysical journal 2005;88(3):1552-9.
2005: Pan Yongping; Ma Buyong; Venkataraghavan R Babu; Levine Arnold J; Nussinov Ruth
In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1.
Biochemistry 2005;44(5):1423-32.
2005: Keskin Ozlem; Ma Buyong; Nussinov Ruth
Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.
Journal of molecular biology 2005;345(5):1281-94.
2005: Haspel Nurit; Zanuy David; Ma Buyong; Wolfson Haim; Nussinov Ruth
A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core.
Journal of molecular biology 2005;345(5):1213-27.
2005: Keskin Ozlem; Nussinov Ruth
Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways.
Protein engineering, design & selection : PEDS 2005;18(1):11-24.
2004: Ma Buyong; Nussinov Ruth
From computational quantum chemistry to computational biology: experiments and computations are (full) partners.
Physical biology 2004;1(3-4):P23-6.
2004: Ma Buyong; Nussinov Ruth
Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes.
The Journal of biological chemistry 2004;279(51):53875-85.
2004: Li Xiang; Keskin Ozlem; Ma Buyong; Nussinov Ruth; Liang Jie
Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.
Journal of molecular biology 2004;344(3):781-95.
2004: Kumar Sandeep; Nussinov Ruth
Experiment-guided thermodynamic simulations on reversible two-state proteins: implications for protein thermostability.
Biophysical chemistry 2004;111(3):235-46.
2004: Gunasekaran K; Ma Buyong; Nussinov Ruth
Is allostery an intrinsic property of all dynamic proteins?
Proteins 2004;57(3):433-43.
2004: Tsai Hui-Hsu Gavin; Tsai Chung-Jung; Ma Buyong; Nussinov Ruth
In silico protein design by combinatorial assembly of protein building blocks.
Protein science : a publication of the Protein Society 2004;13(10):2753-65.
2004: Zanuy David; Gunasekaran K; Ma Buyong; Tsai Hui-Hsu Gavin; Tsai Chung-Jung; Nussinov Ruth
Insights into amyloid structural formation and assembly through computational approaches.
Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis 2004;11(3):143-61.
2004: Barzilai Adi; Kumar Sandeep; Wolfson Haim; Nussinov Ruth
Potential folding-function interrelationship in proteins.
Proteins 2004;56(4):635-49.
2004: Gunasekaran Kannan; Tsai Chung-Jung; Nussinov Ruth
Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers.
Journal of molecular biology 2004;341(5):1327-41.
2004: Tsai Hui-Hsu; Zanuy David; Haspel Nurit; Gunasekaran Kannan; Ma Buyong; Tsai Chung-Jung; Nussinov Ruth
The stability and dynamics of the human calcitonin amyloid peptide DFNKF.
Biophysical journal 2004;87(1):146-58.
2004: Shatsky Maxim; Dror Oranit; Schneidman-Duhovny Dina; Nussinov Ruth; Wolfson Haim J
BioInfo3D: a suite of tools for structural bioinformatics.
Nucleic acids research 2004;32(Web Server issue):W503-7.
2004: Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
A method for simultaneous alignment of multiple protein structures.
Proteins 2004;56(1):143-56.
2004: Pan Yongping; Ma Buyong; Keskin Ozlem; Nussinov Ruth
Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain.
The Journal of biological chemistry 2004;279(29):30523-30.
2004: Zanuy David; Haspel Nurit; Tsai Hui-Hsu Gavin; Ma Buyong; Gunasekaran Kannan; Wolfson Haim J; Nussinov Ruth
Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19.
Physical biology 2004;1(1-2):89-99.
2004: Halperin Inbal; Wolfson Haim; Nussinov Ruth
Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking.
Structure (London, England : 1993) 2004;12(6):1027-38.
2004: Shulman-Peleg Alexandra; Nussinov Ruth; Wolfson Haim J
Recognition of functional sites in protein structures.
Journal of molecular biology 2004;339(3):607-33.
2004: Keskin Ozlem; Tsai Chung-Jung; Wolfson Haim; Nussinov Ruth
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.
Protein science : a publication of the Protein Society 2004;13(4):1043-55.
2004: Zanuy David; Porat Yair; Gazit Ehud; Nussinov Ruth
Peptide sequence and amyloid formation; molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs.
Structure (London, England : 1993) 2004;12(3):439-55.
2004: Kumar Sandeep; Nussinov Ruth
Different roles of electrostatics in heat and in cold: adaptation by citrate synthase.
Chembiochem : a European journal of chemical biology 2004;5(3):280-90.
2004: Gunasekaran Kannan; Nussinov Ruth
Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions.
Chembiochem : a European journal of chemical biology 2004;5(2):224-30.
2004: Schneidman-Duhovny Dina; Nussinov Ruth; Wolfson Haim J
Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking.
Current medicinal chemistry 2004;11(1):91-107.
2004: Dror Oranit; Shulman-Peleg Alexandra; Nussinov Ruth; Wolfson Haim J
Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design.
Current medicinal chemistry 2004;11(1):71-90.
2004: Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
FlexProt: alignment of flexible protein structures without a predefinition of hinge regions.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(1):83-106.
2003: Dror Oranit; Benyamini Hadar; Nussinov Ruth; Wolfson Haim J
Multiple structural alignment by secondary structures: algorithm and applications.
Protein science : a publication of the Protein Society 2003;12(11):2492-507.
2003: Gunasekaran K; Ma Buyong; Nussinov Ruth
Triggering loops and enzyme function: identification of loops that trigger and modulate movements.
Journal of molecular biology 2003;332(1):143-59.
2003: Ma Buyong; Nussinov Ruth
Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences.
Protein science : a publication of the Protein Society 2003;12(9):1882-93.
2003: Oron Assaf; Wolfson Haim; Gunasekaran Kannan; Nussinov Ruth
Using DelPhi to compute electrostatic potentials and assess their contribution to interactions.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2003;Chapter 8():Unit 8.4.
2003: Ma Buyong; Nussinov Ruth
Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants.
Protein engineering 2003;16(8):561-75.
2003: Halperin Inbal; Wolfson Haim; Nussinov Ruth
SiteLight: binding-site prediction using phage display libraries.
Protein science : a publication of the Protein Society 2003;12(7):1344-59.
2003: Schneidman-Duhovny Dina; Inbar Yuval; Polak Vladimir; Shatsky Maxim; Halperin Inbal; Benyamini Hadar; Barzilai Adi; Dror Oranit; Haspel Nurit; Nussinov Ruth; Wolfson Haim J
Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking.
Proteins 2003;52(1):107-12.
2003: Benyamini Hadar; Gunasekaran K; Wolfson Haim; Nussinov Ruth
Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques.
Journal of molecular biology 2003;330(1):159-74.
2003: Zanuy David; Nussinov Ruth
The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29.
Journal of molecular biology 2003;329(3):565-84.
2003: Haspel Nurit; Tsai Chung-Jung; Wolfson Haim; Nussinov Ruth
Reducing the computational complexity of protein folding via fragment folding and assembly.
Protein science : a publication of the Protein Society 2003;12(6):1177-87.
2003: Ma Buyong; Elkayam Tal; Wolfson Haim; Nussinov Ruth
Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(10):5772-7.
2003: Kumar Sandeep; Tsai Chung Jung; Nussinov Ruth
Temperature range of thermodynamic stability for the native state of reversible two-state proteins.
Biochemistry 2003;42(17):4864-73.
2003: Benyamini Hadar; Gunasekaran K; Wolfson Haim; Nussinov Ruth
Conservation and amyloid formation: a study of the gelsolin-like family.
Proteins 2003;51(2):266-82.
2003: Haspel Nurit; Tsai Chung-Jung; Wolfson Haim; Nussinov Ruth
Hierarchical protein folding pathways: a computational study of protein fragments.
Proteins 2003;51(2):203-15.
2003: Gunasekaran K; Ma Buyong; Ramakrishnan B; Qasba Pradman K; Nussinov Ruth
Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I.
Biochemistry 2003;42(13):3674-87.
2003: Zanuy David; Ma Buyong; Nussinov Ruth
Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL.
Biophysical journal 2003;84(3):1884-94.
2003: Gunasekaran Kannan; Tsai Chung-Jung; Kumar Sandeep; Zanuy David; Nussinov Ruth
Extended disordered proteins: targeting function with less scaffold.
Trends in biochemical sciences 2003;28(2):81-5.
2003: Inbar Yuval; Benyamini Hadar; Nussinov Ruth; Wolfson Haim J
Protein structure prediction via combinatorial assembly of sub-structural units.
Bioinformatics (Oxford, England) 2003;19 Suppl 1():i158-68.
2003: Dror O; Benyamini H; Nussinov R; Wolfson H
MASS: multiple structural alignment by secondary structures.
Bioinformatics (Oxford, England) 2003;19 Suppl 1():i95-104.
2002: Ma Buyong; Nussinov Ruth
Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(22):14126-31.
2002: Ma Buyong; Nussinov Ruth
Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation.
Protein science : a publication of the Protein Society 2002;11(10):2335-50.
2002: Kumar Sandeep; Nussinov Ruth
Relationship between ion pair geometries and electrostatic strengths in proteins.
Biophysical journal 2002;83(3):1595-612.
2002: Shatsky Maxim; Nussinov Ruth; Wolfson Haim J
Flexible protein alignment and hinge detection.
Proteins 2002;48(2):242-56.
2002: Kumar Sandeep; Nussinov Ruth
Close-range electrostatic interactions in proteins.
Chembiochem : a European journal of chemical biology 2002;3(7):604-17.
2002: Tsai Chung-Jung; Polverino de Laureto Patrizia; Fontana Angelo; Nussinov Ruth
Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins.
Protein science : a publication of the Protein Society 2002;11(7):1753-70.
2002: Halperin Inbal; Ma Buyong; Wolfson Haim; Nussinov Ruth
Principles of docking: An overview of search algorithms and a guide to scoring functions.
Proteins 2002;47(4):409-43.
2002: Kumar Sandeep; Tsai Chung-Jung; Nussinov Ruth
Maximal stabilities of reversible two-state proteins.
Biochemistry 2002;41(17):5359-74.
2002: Sham Yuk Yin; Ma Buyong; Tsai Chung-Jung; Nussinov Ruth
Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway.
Proteins 2002;46(3):308-20.
2002: Ma Buyong; Shatsky Maxim; Wolfson Haim J; Nussinov Ruth
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations.
Protein science : a publication of the Protein Society 2002;11(2):184-97.
2002: Tsai Chung-Jung; Maizel Jacob V; Nussinov Ruth
The hydrophobic effect: a new insight from cold denaturation and a two-state water structure.
Critical reviews in biochemistry and molecular biology 2002;37(2):55-69.
2001: Kumar S; Tsai C J; Nussinov R
Thermodynamic differences among homologous thermophilic and mesophilic proteins.
Biochemistry 2001;40(47):14152-65.
2001: Kumar S; Nussinov R
How do thermophilic proteins deal with heat?
Cellular and molecular life sciences : CMLS 2001;58(9):1216-33.
2001: Kumar S; Nussinov R
Fluctuations in ion pairs and their stabilities in proteins.
Proteins 2001;43(4):433-54.
2001: Kumar S; Sham Y Y; Tsai C J; Nussinov R
Protein folding and function: the N-terminal fragment in adenylate kinase.
Biophysical journal 2001;80(5):2439-54.
2001: Leibowitz N; Fligelman Z Y; Nussinov R; Wolfson H J
Automated multiple structure alignment and detection of a common substructural motif.
Proteins 2001;43(3):235-45.
2001: Sham Y Y; Ma B; Tsai C J; Nussinov R
Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations.
Protein science : a publication of the Protein Society 2001;10(1):135-48.
2001: Leibowitz N; Nussinov R; Wolfson H J
MUSTA--a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins.
Journal of computational biology : a journal of computational molecular cell biology 2001;8(2):93-121.
2000: Kumar S; Nussinov R
Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper.
Proteins 2000;41(4):485-97.
2000: Buyong; Xiong J; Lubkowski J; Nussinov R
Homology modeling and molecular dynamics simulations of lymphotactin.
Protein science : a publication of the Protein Society 2000;9(11):2192-9.
2000: Ma B; Tsai C J; Nussinov R
A systematic study of the vibrational free energies of polypeptides in folded and random states.
Biophysical journal 2000;79(5):2739-53.
2000: Ma B; Tsai C J; Nussinov R
Binding and folding: in search of intramolecular chaperone-like building block fragments.
Protein engineering 2000;13(9):617-27.
2000: Ma B; Nussinov R
Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces.
Journal of molecular biology 2000;296(4):1091-104.
2000: Kumar S; Ma B; Tsai C J; Sinha N; Nussinov R
Folding and binding cascades: dynamic landscapes and population shifts.
Protein science : a publication of the Protein Society 2000;9(1):10-9.
2000: Wolfson H J; Nussinov R
Geometrical docking algorithms. A practical approach.
Methods in molecular biology (Clifton, N.J.) 2000;143():377-97.
2000: Shatsky M; Fligelman Z Y; Nussinov R; Wolfson H J
Alignment of flexible protein structures.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 2000;8():329-43.
1999: Kumar S; Nussinov R
Salt bridge stability in monomeric proteins.
Journal of molecular biology 1999;293(5):1241-55.
1999: Ma B; Nussinov R
Explicit and implicit water simulations of a beta-hairpin peptide.
Proteins 1999;37(1):73-87.
1999: Ma B; Kumar S; Tsai C J; Nussinov R
Folding funnels and binding mechanisms.
Protein engineering 1999;12(9):713-20.
1999: Norel R; Wolfson H J; Nussinov R
Small molecule recognition: solid angles surface representation and molecular shape complementarity.
Combinatorial chemistry & high throughput screening 1999;2(4):223-37.
1999: Tsai C J; Maizel J V; Nussinov R
Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding.
Protein science : a publication of the Protein Society 1999;8(8):1591-604.
1999: Norel R; Petrey D; Wolfson H J; Nussinov R
Examination of shape complementarity in docking of unbound proteins.
Proteins 1999;36(3):307-17.
1999: Tsai C J; Kumar S; Ma B; Nussinov R
Folding funnels, binding funnels, and protein function.
Protein science : a publication of the Protein Society 1999;8(6):1181-90.
1999: Verbitsky G; Nussinov R; Wolfson H
Flexible structural comparison allowing hinge-bending, swiveling motions.
Proteins 1999;34(2):232-54.
1999: Leibowitz N; Fligelman Z Y; Nussinov R; Wolfson H J
Multiple structural alignment and core detection by geometric hashing.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():169-77.
1999: Kumar S; Ma B; Tsai C J; Wolfson H; Nussinov R
Folding funnels and conformational transitions via hinge-bending motions.
Cell biochemistry and biophysics 1999;31(2):141-64.
1998: Sandak B; Wolfson H J; Nussinov R
Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers.
Proteins 1998;32(2):159-74.
1998: Li A J; Nussinov R
A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking.
Proteins 1998;32(1):111-27.
1998: Lin S L; Xu D; Li A; Nussinov R
Electrostatics, allostery, and activity of the yeast chorismate mutase.
Proteins 1998;31(4):445-52.
1998: Rosen M; Lin S L; Wolfson H; Nussinov R
Molecular shape comparisons in searches for active sites and functional similarity.
Protein engineering 1998;11(4):263-77.
1998: Xu D; Tsai C J; Nussinov R
Mechanism and evolution of protein dimerization.
Protein science : a publication of the Protein Society 1998;7(3):533-44.
1998: Sandak B; Nussinov R; Wolfson H J
A method for biomolecular structural recognition and docking allowing conformational flexibility.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(4):631-54.
1997: Azarya-Sprinzak E; Naor D; Wolfson H J; Nussinov R
Interchanges of spatially neighbouring residues in structurally conserved environments.
Protein engineering 1997;10(10):1109-22.
1997: Tsai C J; Xu D; Nussinov R
Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes.
Protein science : a publication of the Protein Society 1997;6(9):1793-805.
1997: Lin S L; Xu D; Li A; Rosen M; Wolfson H J; Nussinov R
Investigation of the enzymatic mechanism of the yeast chorismate mutase by docking a transition state analog.
Journal of molecular biology 1997;271(5):838-45.
1997: Tsai C J; Nussinov R
Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association.
Protein science : a publication of the Protein Society 1997;6(7):1426-37.
1997: Tsai C J; Lin S L; Wolfson H J; Nussinov R
Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect.
Protein science : a publication of the Protein Society 1997;6(1):53-64.
1997: Tsai C J; Nussinov R
Hydrophobic folding units derived from dissimilar monomer structures and their interactions.
Protein science : a publication of the Protein Society 1997;6(1):24-42.
1996: Alesker V; Nussinov R; Wolfson H J
Detection of non-topological motifs in protein structures.
Protein engineering 1996;9(12):1103-19.
1996: Tsai C J; Lin S L; Wolfson H J; Nussinov R
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique.
Journal of molecular biology 1996;260(4):604-20.
1996: Tsai C J; Lin S L; Wolfson H J; Nussinov R
Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences.
Critical reviews in biochemistry and molecular biology 1996;31(2):127-52.
1996: Naor D; Fischer D; Jernigan R L; Wolfson H J; Nussinov R
Amino acid pair interchanges at spatially conserved locations.
Journal of molecular biology 1996;256(5):924-38.
1995: Fischer D; Tsai C J; Nussinov R; Wolfson H
A 3D sequence-independent representation of the protein data bank.
Protein engineering 1995;8(10):981-97.
1995: Norel R; Lin S L; Wolfson H J; Nussinov R
Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking.
Journal of molecular biology 1995;252(2):263-73.
1995: Fischer D; Lin S L; Wolfson H L; Nussinov R
A geometry-based suite of molecular docking processes.
Journal of molecular biology 1995;248(2):459-77.
1995: Lin S L; Tsai C J; Nussinov R
A study of four-helix bundles: investigating protein folding via similar architectural motifs in protein cores and in subunit interfaces.
Journal of molecular biology 1995;248(1):151-61.
1995: Sandak B; Nussinov R; Wolfson H J
An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching.
Computer applications in the biosciences : CABIOS 1995;11(1):87-99.
1994: Norel R; Lin S L; Wolfson H J; Nussinov R
Shape complementarity at protein-protein interfaces.
Biopolymers 1994;34(7):933-40.
1994: Fischer D; Wolfson H; Lin S L; Nussinov R
Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.
Protein science : a publication of the Protein Society 1994;3(5):769-78.
1994: Norel R; Fischer D; Wolfson H J; Nussinov R
Molecular surface recognition by a computer vision-based technique.
Protein engineering 1994;7(1):39-46.
1993: Fischer D; Wolfson H; Nussinov R
Spatial, sequence-order-independent structural comparison of alpha/beta proteins: evolutionary implications.
Journal of biomolecular structure & dynamics 1993;11(2):367-80.
1993: Fischer D; Norel R; Wolfson H; Nussinov R
Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition.
Proteins 1993;16(3):278-92.
1993: Bachar O; Fischer D; Nussinov R; Wolfson H
A computer vision based technique for 3-D sequence-independent structural comparison of proteins.
Protein engineering 1993;6(3):279-88.
1992: Fischer D; Bachar O; Nussinov R; Wolfson H
An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins.
Journal of biomolecular structure & dynamics 1992;9(4):769-89.
1991: Nussinov R; Wolfson H J
Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(23):10495-9.
1990: Nussinov R
Sequence signals in eukaryotic upstream regions.
Critical reviews in biochemistry and molecular biology 1990;25(3):185-224.
1989: Nussinov R
Conserved signals around the 5' splice sites in eukaryotic nuclear precursor mRNAs: G-runs are frequent in the introns and C in the exons near both 5' and 3' splice sites.
Journal of biomolecular structure & dynamics 1989;6(5):985-1000.
1988: Landau G M; Vishkin U; Nussinov R
Locating alignments with k differences for nucleotide and amino acid sequences.
Computer applications in the biosciences : CABIOS 1988;4(1):19-24.
1987: Nussinov R
(A)GGG(A), (A)CCC(A) and other potential 3' splice signals in primate nuclear pre-mRNA sequences.
Biochimica et biophysica acta 1987;910(3):261-70.
1987: Landau G M; Vishkin U; Nussinov R
An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences.
Journal of theoretical biology 1987;126(4):483-90.
1987: Nussinov R
Conserved putative signals in 3' intron junctions in rodents.
Journal of biomolecular structure & dynamics 1987;4(6):1051-64.
1987: Nussinov R
Theoretical molecular biology: prospectives and perspectives.
Journal of theoretical biology 1987;125(2):219-35.
1985: Nussinov R
The predicted presence of large helical structural variation in yeast HIS4 upstream region is correlated with general amino acid control on the CYC1 gene.
Journal of biomolecular structure & dynamics 1985;3(2):349-61.

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