-Ruth Nussinov Researcher Activity Profile

Research Author Detailed Information 

Ruth Nussinov Publication Rate By Year

Ruth Nussinov has published 4 paper(s) in 2005, 15 paper(s) in 2006, 35 paper(s) in 2007, 12 paper(s) in 2008, for a total of 66 research publications in total.

Ruth R Nussinov Author Information

LAST NAME: nussinov

FIRST NAME: Ruth

INITIALS: r

AFFILIATION:

Papers

Ruth Nussinov's Publication Record

1. Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. Year Published: 2007
Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA. jangh@ncifcrf.gov <jangh@ncifcrf.gov>
2. ARTS: alignment of RNA tertiary structures. Year Published: 2005
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel. oranit@post.tau.ac.il
3. Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Year Published: 2005
Koc University, Center for Computational Biology and Bioinformatics, and College of Engineering, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.
4. The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins. Year Published: 2005
Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Frederick, MD 21702, USA. mab@ncifcrf.gov
5. Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies. Year Published: 2005
School of Computer Science, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. inbaryuv@tau.ac.il
6. Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids. Year Published: 2006
7. From peptide-based material science to protein fibrils: discipline convergence in nanobiology. Year Published: 2006
8. Designing a nanotube using naturally occurring protein building blocks. Year Published: 2006
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research, Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America.
9. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Year Published: 2006
Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA.
10. Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Year Published: 2006
Bioinformatics Research Unit, Research and Development Division, Tokyo, Japan. ao-mesa@fujirebio.co.jp
11. A hierarchical protein folding scheme based on the building block folding model. Year Published: 2006
Department of Exact Sciences, School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
12. Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Year Published: 2006
Basic Research Program, SAIC-Frederick Inc, Center for Cancer Research, Nanobiology Program, NCI-Frederick, Frederick MD 21702, USA.
13. Structure by design: from single proteins and their building blocks to nanostructures. Year Published: 2006
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA.
14. Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Year Published: 2006
Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA.
15. Association of putative concave protein-binding sites with the fluctuation behavior of residues. Year Published: 2006
Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek 34342, Istanbul, Turkey.
16. Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure. Year Published: 2006
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA.
17. Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid. Year Published: 2006
18. 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. Year Published: 2006
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA. guna.kannan@yahoo.com
19. "Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains. Year Published: 2006
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland 21702, USA.
20. Structural basis for p53 binding-induced DNA bending. Year Published: 2007
Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, USA.
21. Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues. Year Published: 2007
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-FCRDC, Frederick, Maryland 21702, USA.
22. EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps. Year Published: 2007
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Israel. kerenl@post.tau.ac.il
23. Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4. Year Published: 2007
Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
24. Intrinsic conformational characteristics of alpha,alpha-diphenylglycine. Year Published: 2007
25. Similar binding sites and different partners: implications to shared proteins in cellular pathways. Year Published: 2007
Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.
26. Use of constrained synthetic amino acids in beta-helix proteins for conformational control. Year Published: 2007
27. Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. Year Published: 2007
28. Conformations of proline analogues having double bonds in the ring. Year Published: 2007
29. Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Year Published: 2007
Basic Research Program, SAIC-Frederick Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA. mab@ncifcrf.gov
30. Towards drugs targeting multiple proteins in a systems biology approach. Year Published: 2007
Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.
31. Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Year Published: 2007
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA. mab@ncifcrf.gov
32. Principles of nanostructure design with protein building blocks. Year Published: 2007
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA.
33. Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer. Year Published: 2007
School of Computer Science Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
34. Comprehensive analysis of co-occurring domain sets in yeast proteins. Year Published: 2007
Sackler Institute of Molecular Medicine, Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. inbarg@tau.ac.il <inbarg@tau.ac.il>
35. Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages. Year Published: 2007
Bioinformatics Research Unit, Research and Development Division, Fujirebio Inc, Komiya-cho, Hachioji-shi, Tokyo 192-0031, Japan. ao-mesa@fujirebio.co.jp
36. Ligand binding and circular permutation modify residue interaction network in DHFR. Year Published: 2007
Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Washington, District of Columbia, United States of America.
37. Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Year Published: 2007
Center for Cancer Research Nanobiology Program, SAIC-Frederick, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
38. FireDock: fast interaction refinement in molecular docking. Year Published: 2007
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
39. Coarse-grained representation of beta-helical protein building blocks. Year Published: 2007
40. Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. Year Published: 2007
41. Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics study. Year Published: 2007
42. Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Year Published: 2007
Basic Research Program, SAIC-Frederick Center for Cancer Research, Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA.
43. Automatic prediction of protein interactions with large scale motion. Year Published: 2007
School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. duhovka@post.tau.ac.il
44. Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. Year Published: 2007
45. Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment. Year Published: 2007
46. Principles of nanostructure design with protein building blocks. Year Published: 2007
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA.
47. Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Year Published: 2007
Basic Research Program, SAIC-Frederick Center for Cancer Research, Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA.
48. Ligand binding and circular permutation modify residue interaction network in DHFR. Year Published: 2007
Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Washington, District of Columbia, United States of America.
49. Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics study. Year Published: 2007
50. Automatic prediction of protein interactions with large scale motion. Year Published: 2007
School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. duhovka@post.tau.ac.il
51. Atomic-level description of amyloid beta-dimer formation. Year Published: 2006
Los Alamos National Laboratory, T-10, MS K710, Los Alamos, New Mexico 87545, USA.
52. Coarse-graining the self-assembly of beta-helical protein building blocks. Year Published: 2007
53. QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding. Year Published: 2007
Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
54. Spatial chemical conservation of hot spot interactions in protein-protein complexes. Year Published: 2008
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University, Tel Aviv 69978, Israel. shulmana@tau.ac.il
55. Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Year Published: 2008
Basic Research Program, Science Applications International Corporation (SAIC)-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702.
56. Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Year Published: 2008
Basic Research Program, Science Applications International Corporation (SAIC)-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
57. Coarse-graining the self-assembly of beta-helical protein building blocks. Year Published: 2007
Departament d'Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain. curco@angel.qui.ub.es
58. New structures help the modeling of toxic amyloidss ion channels. Year Published: 2008
Center for Cancer Research Nanobiology Program, SAIC-Frederick Inc. NCI-Frederick, Frederick, MD 21702, USA.
59. Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Year Published: 2008
Basic Research Program, Science Applications International Corporation (SAIC)-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
60. 1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue. Year Published: 2008
Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II No. 69, Lleida E-25001, Spain. jcasanovas@quimica.udl.cat
61. 1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue. Year Published: 2008
62. Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific. Year Published: 2008
Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA. zhengj@uakron.edu
63. Spatial chemical conservation of hot spot interactions in protein-protein complexes. Year Published: 2008
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University, Tel Aviv 69978, Israel. shulmana@tau.ac.il
64. HingeProt: automated prediction of hinges in protein structures. Year Published: 2008
65. Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play. Year Published: 2008
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA.
66. Allostery: absence of a change in shape does not imply that allostery is not at play. Year Published: 2008
Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA.