Ruth Nussinov
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Biology Physics
Ruth Nussinov's Degrees
- PhD Biophysics Weizmann Institute of Science
- Masters Biophysics Weizmann Institute of Science
Why Is Ruth Nussinov Influential?
(Suggest an Edit or Addition)According to Wikipedia, Ruth Nussinov is an Israeli-American biologist born in Rehovot who works as a Professor in the Department of Human Genetics, School of Medicine at Tel Aviv University and is the Senior Principal Scientist and Principal Investigator at the National Cancer Institute, National Institutes of Health. Nussinov is also the Editor in Chief of the Current Opinion in Structural Biology and formerly of the journal PLOS Computational Biology.
Ruth Nussinov's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- PatchDock and SymmDock: servers for rigid and symmetric docking (2005) (2512)
- The role of dynamic conformational ensembles in biomolecular recognition. (2009) (1621)
- Principles of docking: An overview of search algorithms and a guide to scoring functions (2002) (1233)
- Factors enhancing protein thermostability. (2000) (860)
- Shape complementarity at protein–protein interfaces (1994) (837)
- Is allostery an intrinsic property of all dynamic proteins? (2004) (789)
- Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review (2012) (755)
- Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. (2010) (711)
- Efficient Unbound Docking of Rigid Molecules (2002) (684)
- FireDock: a web server for fast interaction refinement in molecular docking† (2008) (640)
- FireDock: Fast interaction refinement in molecular docking (2007) (628)
- Folding funnels, binding funnels, and protein function (1999) (614)
- Aβ(1–42) Fibril Structure Illuminates Self-recognition and Replication of Amyloid in Alzheimer’s (2015) (603)
- Algorithms for Loop Matchings (1978) (599)
- Fast algorithm for predicting the secondary structure of single-stranded RNA. (1980) (585)
- Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces (2003) (571)
- Folding and binding cascades: Dynamic landscapes and population shifts (2008) (562)
- Principles of protein-protein interactions: what are the preferred ways for proteins to interact? (2008) (553)
- Allostery in Disease and in Drug Discovery (2013) (542)
- Folding funnels and binding mechanisms. (1999) (541)
- Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. (2005) (477)
- A method for simultaneous alignment of multiple protein structures (2004) (465)
- Close‐Range Electrostatic Interactions in Proteins (2002) (434)
- How do thermophilic proteins deal with heat? (2001) (428)
- Hydrogen bonds and salt bridges across protein-protein interfaces. (1997) (425)
- Allostery: absence of a change in shape does not imply that allostery is not at play. (2008) (422)
- Salt bridge stability in monomeric proteins. (1999) (412)
- Studies of protein‐protein interfaces: A statistical analysis of the hydrophobic effect (1997) (408)
- Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ16–22, Aβ16–35, and Aβ10–35): Sequence effects (2002) (378)
- Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations (2002) (373)
- The origin of allosteric functional modulation: multiple pre-existing pathways. (2009) (339)
- Folding and binding cascades: shifts in energy landscapes. (1999) (334)
- Extended disordered proteins: targeting function with less scaffold. (2003) (329)
- A Unified View of “How Allostery Works” (2014) (310)
- Residues crucial for maintaining short paths in network communication mediate signaling in proteins (2006) (307)
- Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms (2009) (297)
- Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. (1991) (295)
- Conservation of polar residues as hot spots at protein interfaces (2000) (292)
- Recognition of Functional Sites in Protein Structures☆ (2004) (270)
- Artificial intelligence in COVID-19 drug repurposing (2020) (267)
- Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states (2010) (266)
- Taking geometry to its edge: Fast unbound rigid (and hinge‐bent) docking (2003) (254)
- Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM (2011) (253)
- Polymorphism in Alzheimer Aβ Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape (2010) (252)
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. (2016) (248)
- The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. (2016) (246)
- Protein binding versus protein folding: the role of hydrophilic bridges in protein associations. (1997) (245)
- Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. (2008) (242)
- deepDR: a network-based deep learning approach to in silico drug repositioning (2019) (239)
- Ras Conformational Ensembles, Allostery, and Signaling. (2016) (238)
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. (2021) (236)
- What’s in a name? Why these proteins are intrinsically disordered (2013) (216)
- HingeProt: Automated prediction of hinges in protein structures (2008) (214)
- Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. (2006) (213)
- PRISM: protein interactions by structural matching (2005) (213)
- PharmaGist: a webserver for ligand-based pharmacophore detection (2008) (212)
- Geometry‐based flexible and symmetric protein docking (2005) (204)
- A geometry-based suite of molecular docking processes. (1995) (199)
- A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications (2004) (196)
- Dynamic allostery: linkers are not merely flexible. (2011) (196)
- Allostery in Its Many Disguises: From Theory to Applications. (2019) (196)
- Relationship between ion pair geometries and electrostatic strengths in proteins. (2002) (195)
- Enzyme dynamics point to stepwise conformational selection in catalysis. (2010) (194)
- Principles of flexible protein–protein docking (2008) (193)
- Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. (2004) (189)
- Truncated β-amyloid peptide channels provide an alternative mechanism for Alzheimer’s Disease and Down syndrome (2010) (189)
- Structured disorder and conformational selection (2001) (188)
- Antimicrobial properties of amyloid peptides. (2012) (180)
- A survey of available tools and web servers for analysis of protein-protein interactions and interfaces (2008) (178)
- Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. (2015) (175)
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics (2016) (172)
- FiberDock: Flexible induced‐fit backbone refinement in molecular docking (2010) (170)
- Molecular dynamics simulations of alanine rich β‐sheet oligomers: Insight into amyloid formation (2002) (168)
- Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. (2007) (168)
- GTP-Dependent K-Ras Dimerization. (2015) (168)
- A set of van der Waals and coulombic radii of protein atoms for molecular and solvent‐accessible surface calculation, packing evaluation, and docking (1998) (167)
- Allostery and population shift in drug discovery. (2010) (167)
- A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. (1996) (166)
- Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. (2011) (166)
- Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. (2004) (166)
- Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. (2007) (165)
- Allosteric post-translational modification codes. (2012) (165)
- Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. (2015) (163)
- Allostery without a conformational change? Revisiting the paradigm. (2015) (162)
- A computer vision based technique for 3-D sequence-independent structural comparison of proteins. (1993) (159)
- PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes (2014) (159)
- Examination of shape complementarity in docking of Unbound proteins (1999) (158)
- Allostery: An Overview of Its History, Concepts, Methods, and Applications (2016) (157)
- The underappreciated role of allostery in the cellular network. (2013) (154)
- Topological properties of protein interaction networks from a structural perspective. (2008) (148)
- Similar binding sites and different partners: implications to shared proteins in cellular pathways. (2007) (145)
- Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers (2000) (143)
- Tree graphs of RNA secondary structures and their comparisons. (1989) (142)
- Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. (2004) (142)
- Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non‐enzyme families (2006) (141)
- New structures help the modeling of toxic amyloidbeta ion channels. (2008) (140)
- Doublet frequencies in evolutionary distinct groups. (1984) (140)
- Nanoparticle-induced vascular blockade in human prostate cancer. (2010) (140)
- Flexible protein alignment and hinge detection (2002) (140)
- Atomic-Level Description of Amyloid β-Dimer Formation (2006) (138)
- Mechanisms of transcription factor selectivity. (2010) (136)
- Target identification among known drugs by deep learning from heterogeneous networks (2020) (134)
- The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B (2016) (133)
- MASS: multiple structural alignment by secondary structures (2003) (129)
- Protein-protein interaction networks: how can a hub protein bind so many different partners? (2009) (128)
- Allo-network drugs: harnessing allostery in cellular networks. (2011) (128)
- Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. (2004) (128)
- MolAxis: Efficient and accurate identification of channels in macromolecules (2008) (127)
- Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. (1996) (127)
- An integrated suite of fast docking algorithms (2010) (127)
- Molecular surface representations by sparse critical points (1994) (124)
- Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers (1998) (124)
- Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin‐Dockerin families (2006) (124)
- Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. (2006) (123)
- Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view. (2016) (122)
- How do thermophilic proteins deal with heat? Cell Mol Life Sci (2001) (121)
- Hydrophobic folding units at protein‐protein interfaces: Implications to protein folding and to protein‐protein association (1997) (121)
- Sequence dependence of DNA conformational flexibility. (1989) (121)
- Molecular surface recognition by a computer vision-based technique. (1994) (120)
- Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's β-amyloid peptide: relevance to the ion channel mechanism of AD pathology. (2012) (118)
- Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. (1995) (117)
- Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane. (2013) (117)
- Thermodynamic differences among homologous thermophilic and mesophilic proteins. (2001) (114)
- Mutations in LZTR1 drive human disease by dysregulating RAS ubiquitination (2018) (114)
- β-Barrel topology of Alzheimer's β-amyloid ion channels. (2010) (114)
- 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. (2007) (113)
- Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link. (2011) (113)
- The Hydrophobic Effect: A New Insight from Cold Denaturation and a Two-State Water Structure (2002) (113)
- Architectures and functional coverage of protein-protein interfaces. (2008) (112)
- Protein functional epitopes: hot spots, dynamics and combinatorial libraries. (2001) (111)
- Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. (2000) (110)
- Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. (2005) (109)
- Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. (2003) (109)
- Principles of Allosteric Interactions in Cell Signaling (2014) (107)
- An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. (1992) (107)
- The NRF2‐related interactome and regulome contain multifunctional proteins and fine‐tuned autoregulatory loops (2012) (106)
- Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. (1996) (106)
- Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism (2009) (104)
- 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 (1994) (103)
- Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications (2009) (103)
- Point mutations and sequence variability in proteins: Redistributions of preexisting populations (2001) (103)
- FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking (2010) (103)
- Mechanism and evolution of protein dimerization (1998) (102)
- Unraveling structural mechanisms of allosteric drug action. (2014) (101)
- Molecular shape comparisons in searches for active sites and functional similarity. (1998) (100)
- Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor. (2013) (99)
- Protein–protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach (2005) (98)
- SiteEngines: recognition and comparison of binding sites and protein–protein interfaces (2005) (97)
- Multiple conformational selection and induced fit events take place in allosteric propagation. (2014) (96)
- Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane (2017) (96)
- MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions (2008) (96)
- Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. (2008) (95)
- Computational network biology: Data, models, and applications (2020) (95)
- Hydrophobic folding units derived from dissimilar monomer structures and their interactions (1997) (94)
- Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. (2003) (93)
- Prediction of multimolecular assemblies by multiple docking. (2005) (91)
- The design of covalent allosteric drugs. (2015) (91)
- Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages (2007) (91)
- Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. (2007) (90)
- Metal binding sites in amyloid oligomers: Complexes and mechanisms (2012) (88)
- Introduction to Protein Ensembles and Allostery. (2016) (88)
- Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels. (2009) (87)
- Synergistic Interactions between Repeats in Tau Protein and Aβ Amyloids May Be Responsible for Accelerated Aggregation via Polymorphic States (2011) (87)
- Pathogenic Autoreactive T and B Cells Cross-React with Mimotopes Expressed by a Common Human Gut Commensal to Trigger Autoimmunity. (2019) (86)
- The molecular basis of targeting protein kinases in cancer therapeutics. (2013) (85)
- Hollow core of Alzheimer’s Aβ42 amyloid observed by cryoEM is relevant at physiological pH (2010) (85)
- Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region* (2015) (85)
- Maximal stabilities of reversible two-state proteins. (2002) (85)
- The different ways through which specificity works in orthosteric and allosteric drugs. (2012) (85)
- PRISM: protein-protein interaction prediction by structural matching. (2008) (85)
- Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation. (2009) (84)
- Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers (2019) (84)
- The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway (2015) (83)
- Eukaryotic dinucleotide preference rules and their implications for degenerate codon usage. (1981) (82)
- The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. (2003) (81)
- Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules (2007) (81)
- Different Roles of Electrostatics in Heat and in Cold: Adaptation by Citrate Synthase (2004) (80)
- A New View of Ras Isoforms in Cancers. (2016) (80)
- ARTS: alignment of RNA tertiary structures (2005) (79)
- A second molecular biology revolution? The energy landscapes of biomolecular function. (2014) (79)
- Origin of DNA helical structure and its sequence dependence. (1988) (79)
- Protein folding via binding and vice versa. (1998) (78)
- MultiProt - A Multiple Protein Structural Alignment Algorithm (2002) (77)
- Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest (2020) (77)
- Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example† †This article is part of a Molecular BioSystems themed issue on Computational and Systems Biology. (2009) (76)
- Allosteric effects in the marginally stable von Hippel–Lindau tumor suppressor protein and allostery-based rescue mutant design (2008) (76)
- Oncogenic Ras Isoforms Signaling Specificity at the Membrane. (2017) (76)
- MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins (2001) (76)
- Spatial chemical conservation of hot spot interactions in protein-protein complexes (2007) (75)
- Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. (2005) (74)
- Surface motifs by a computer vision technique: Searches, detection, and implications for protein–ligand recognition (1993) (74)
- Selective molecular recognition in amyloid growth and transmission and cross-species barriers. (2012) (74)
- Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers. (2016) (74)
- Automated multiple structure alignment and detection of a common substructural motif (2001) (74)
- Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. (2008) (74)
- FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions (2004) (74)
- Structural Insight into Tau Protein’s Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation (2014) (73)
- Nearest neighbor nucleotide patterns. Structural and biological implications. (1981) (73)
- Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape. (2000) (72)
- Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins (2008) (72)
- Peptide sequence and amyloid formation; molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs. (2004) (72)
- The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas (2015) (71)
- Contribution of Salt Bridges Toward Protein Thermostability (2000) (71)
- The Multiple Common Point Set Problem and Its Application to Molecule Binding Pattern Detection (2006) (71)
- Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects. (2002) (71)
- The Structural Basis of ATP as an Allosteric Modulator (2014) (71)
- Structural motifs at protein‐protein interfaces: Protein cores versus two‐state and three‐state model complexes (1997) (70)
- Some rules in the ordering of nucleotides in the DNA. (1980) (70)
- Constructing structural networks of signaling pathways on the proteome scale. (2012) (69)
- A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility (1998) (68)
- Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. (2008) (68)
- 'Latent drivers' expand the cancer mutational landscape. (2015) (68)
- Structural Convergence Among Diverse, Toxic β-Sheet Ion Channels (2010) (67)
- Multiple structural alignment by secondary structures: Algorithm and applications (2003) (67)
- The higher level of complexity of K‐Ras4B activation at the membrane (2016) (66)
- 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. (2005) (66)
- Nuclease activity gives an edge to host‐defense peptide piscidin 3 over piscidin 1, rendering it more effective against persisters and biofilms (2017) (66)
- The structural network of Interleukin-10 and its implications in inflammation and cancer (2014) (66)
- Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. (2006) (65)
- The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer (2014) (65)
- How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. (2005) (64)
- Polymorphism of amyloid β peptide in different environments: implications for membrane insertion and pore formation. (2011) (64)
- Binding of a C-end rule peptide to the neuropilin-1 receptor: a molecular modeling approach. (2011) (64)
- Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions (2014) (64)
- Folding funnels and conformational transitions via hinge-bending motions (2007) (64)
- Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity? (2000) (63)
- GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site* (2015) (63)
- SiteLight: Binding‐site prediction using phage display libraries (2003) (62)
- A New View of Pathway-Driven Drug Resistance in Tumor Proliferation. (2017) (62)
- A 3D sequence-independent representation of the protein data bank. (1995) (62)
- MolAxis: a server for identification of channels in macromolecules (2008) (60)
- PI3K inhibitors: review and new strategies (2020) (60)
- The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions. (2011) (60)
- A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer. (2001) (59)
- Principles of Protein—Protein Interactions: What Are the Preferred Ways for Proteins to Interact? (2008) (59)
- An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. (2014) (59)
- Protein structure prediction via combinatorial assembly of sub-structural units (2003) (59)
- Protein dynamics and conformational selection in bidirectional signal transduction (2012) (59)
- Reducing the computational complexity of protein folding via fragment folding and assembly (2003) (58)
- Amylin-Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease. (2016) (57)
- High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site (2015) (57)
- Conformational Basis for Asymmetric Seeding Barrier in Filaments of Three- and Four-Repeat Tau (2012) (57)
- 'Pathway drug cocktail': targeting Ras signaling based on structural pathways. (2013) (57)
- Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets (2007) (57)
- Anticancer drug resistance: an update and perspective (2021) (57)
- Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks. (2013) (56)
- Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. (2014) (56)
- Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. (2012) (56)
- The structural network of inflammation and cancer: merits and challenges. (2013) (56)
- Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins* (2012) (56)
- Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer. (2014) (56)
- Protein Folding: Binding of Conformationally Fluctuating Building Blocks Via Population Selection (2001) (55)
- The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant. (2006) (54)
- Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review. (2011) (54)
- Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts. (2017) (54)
- The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation (2009) (54)
- Calmodulin and PI3K Signaling in KRAS Cancers. (2017) (53)
- Sequential folding of a messenger RNA molecule. (1981) (53)
- Consensus features in amyloid fibrils: sheet–sheet recognition via a (polar or nonpolar) zipper structure (2006) (53)
- How Does the Reductase Help To Regulate the Catalytic Cycle of Cytochrome P450 3A4 Using the Conserved Water Channel? (2010) (53)
- Conformational ensembles, signal transduction and residue hot spots: application to drug discovery. (2010) (53)
- Allosteric conformational barcodes direct signaling in the cell. (2013) (52)
- Antimicrobial protegrin-1 forms ion channels: molecular dynamic simulation, atomic force microscopy, and electrical conductance studies. (2010) (52)
- The Mechanism of ATP-Dependent Allosteric Protection of Akt Kinase Phosphorylation. (2015) (52)
- Sequence signals in eukaryotic upstream regions. (1986) (52)
- Favorable domain size in proteins. (1998) (52)
- Optimization of multiple‐sequence alignment based on multiple‐structure alignment (2005) (52)
- Inhibitors of Ras–SOS Interactions (2016) (51)
- In silico protein design by combinatorial assembly of protein building blocks (2004) (51)
- Probing Structural Features of Alzheimer’s Amyloid-β Pores in Bilayers Using Site-Specific Amino Acid Substitutions (2012) (51)
- Pharmacological inhibition of dihydroorotate dehydrogenase induces apoptosis and differentiation in acute myeloid leukemia cells (2018) (51)
- Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling. (2018) (50)
- Effects of point substitutions on the structure of toxic Alzheimer's β-amyloid channels: atomic force microscopy and molecular dynamics simulations. (2012) (50)
- An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching (1995) (50)
- Alzheimer's disease: which type of amyloid-preventing drug agents to employ? (2013) (50)
- Analysis and classification of RNA tertiary structures. (2008) (50)
- Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect (2007) (49)
- Oncogenic KRAS signaling and YAP1/β-catenin: Similar cell cycle control in tumor initiation. (2016) (49)
- Generation and analysis of a protein–protein interface data set with similar chemical and spatial patterns of interactions (2005) (49)
- RNA secondary structures: comparison and determination of frequently recurring substructures by consensus (1989) (48)
- Automatic prediction of protein interactions with large scale motion (2007) (48)
- Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies (2005) (47)
- Probing ion channel activity of human islet amyloid polypeptide (amylin). (2012) (47)
- Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm (2015) (47)
- Fast and accurate modeling of protein–protein interactions by combining template‐interface‐based docking with flexible refinement (2012) (47)
- Fluctuations in ion pairs and their stabilities in proteins (2001) (47)
- Principles of nanostructure design with protein building blocks (2007) (46)
- Binding and folding: in search of intramolecular chaperone-like building block fragments. (2000) (46)
- Protein ensembles link genotype to phenotype (2019) (46)
- K3 fragment of amyloidogenic beta(2)-microglobulin forms ion channels: implication for dialysis related amyloidosis. (2009) (46)
- The ARTS web server for aligning RNA tertiary structures (2006) (46)
- Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices. (2006) (46)
- The stability and dynamics of the human calcitonin amyloid peptide DFNKF. (2004) (45)
- Flexible Cullins in Cullin-RING E3 Ligases Allosterically Regulate Ubiquitination* (2011) (45)
- A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway. (2015) (45)
- Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR (2007) (44)
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- A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides (2011) (10)
- Nanobiology: from physics and engineering to biology (2006) (10)
- Protein–Ligand Interactions: Induced Fit (2001) (10)
- Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs. (2022) (10)
- Developments in integrative modeling with dynamical interfaces. (2019) (10)
- Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation (2016) (9)
- Peptide-MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs). (2020) (9)
- Molecular characterization of L-phenylalanine terminated poly(L-lactide) conjugates (2014) (9)
- Sequence Dependence of DNA Conformations: Means and Fluctuations (1988) (9)
- MAPPIS: Multiple 3D Alignment of Protein-Protein Interfaces (2005) (9)
- Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ. (2018) (9)
- Investigation of the interactions between the EphB2 receptor and SNEW peptide variants (2014) (9)
- (A)GGG(A), (A)CCC(A) and other potential 3' splice signals in primate nuclear pre-mRNA sequences. (1987) (9)
- Docking of Conformationally Flexible Proteins (1996) (9)
- Intrinsic conformational preferences of C(alpha,alpha)-dibenzylglycine. (2008) (9)
- Dipeptide analysis of p53 mutations and evolution of p53 family proteins. (2014) (9)
- Periodic structurally similar oligomers are found on one side of the axes of symmetry in the lac, trp, and gal operators. (1984) (9)
- Sequence context of oligomer tracts in eukaryotic DNA: biological and conformational implications. (1988) (9)
- Conservation and amyloid formation: A study of the gelsolin‐like family (2003) (9)
- Three dimensional structure and sequence homology determine splicing sites in eukaryotic precursor RNA. (1980) (8)
- Cullin neddylation may allosterically tune polyubiquitin chain length and topology. (2017) (8)
- Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates (2018) (8)
- Conformational exploration of two peptides and their hybrid polymer conjugates: potentialities as self-aggregating materials. (2012) (8)
- Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide. (2011) (8)
- Investigation of the enzymatic mechanism of the yeast chorismate mutase by docking a transition state analog. (1997) (8)
- My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype (2021) (8)
- Temperature-Dependent Molecular Adaptation Features in Proteins (2007) (8)
- Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation. (2011) (8)
- Discovery of Protein Substructures in EM Maps (2005) (8)
- PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum. (2016) (8)
- Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis. (2005) (8)
- Attractor Structures of Signaling Networks: Consequences of Different Conformational Barcode Dynamics and Their Relations to Network‐Based Drug Design (2014) (8)
- Protein Allostery in Drug Discovery (2019) (8)
- Compilation of eukaryotic sequences around transcription initiation sites. (1986) (8)
- Drugging multiple same-allele driver mutations in cancer (2021) (8)
- A sequence analysis system encompassing rules for DNA helical distortion (1986) (8)
- Interaction of Calmodulin with the cSH2 Domain of the p85 Regulatory Subunit. (2018) (8)
- Coarse-graining the Self-assembly of β-helical Protein Building Blocks (2007) (8)
- Electrostatics, allostery, and activity of the yeast chorismate mutase (1998) (8)
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- Signals in DNA sequences and their potential properties (1991) (7)
- TGTG, G clustering and other signals near non-mammalian vertebrate mRNA 3' termini: some implications. (1986) (7)
- Integrating the intrinsic conformational preferences of noncoded α‐amino acids modified at the peptide bond into the noncoded amino acids database (2011) (7)
- Open Structural Data in Precision Medicine. (2022) (7)
- Trastuzumab Blocks the Receiver Function of HER2 Leading to the Population Shifts of HER2-Containing Homodimers and Heterodimers (2021) (7)
- Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios (2009) (7)
- Nucleotide-Specific Autoinhibition of Full-Length K-Ras4B Identified by Extensive Conformational Sampling (2020) (7)
- The ordering of the nucleotides in DNA: computational problems in molecular biology. (1989) (7)
- Enhancer elements share local homologous twist-angle variations with a helical periodicity. (1984) (7)
- Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants. (2003) (7)
- General nearest neighbor preferences in G/C oligomers interrupted by A/T: correlation with DNA structure. (1990) (7)
- Ca2+-dependent Switch of Calmodulin Interaction Mode with Tandem IQ motifs in The Scaffolding Protein IQGAP1. (2019) (7)
- Physics approaches to protein interactions and gene regulation (2011) (7)
- Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels. (2016) (7)
- Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients. (2017) (7)
- Medin Oligomer Membrane Pore Formation: A Potential Mechanism of Vascular Dysfunction (2020) (7)
- Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. (2007) (7)
- Nanostructure design : methods and protocols (2008) (6)
- From computational quantum chemistry to computational biology: experiments and computations are (full) partners (2004) (6)
- Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue. (2009) (6)
- An efficient code searching for sequence homology and DNA duplication. (1983) (6)
- Protein folds vs. protein folding: Differing questions, different challenges (2022) (6)
- From “What Is?” to “What Isn't?” Computational Biology (2015) (6)
- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics. (2021) (6)
- Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains (2017) (6)
- Nanostructure Design (2008) (6)
- The implications of higher (or lower) success in secondary structure prediction of chain fragments (2005) (6)
- Speeding up the dynamic algorithm for planar RNA folding. (1990) (6)
- Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue. (2009) (6)
- Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation (2022) (6)
- Efficient computational algorithms for docking and for generating and matching a library of functional epitopes II. Computer vision-based techniques for the generation and utilization of functional epitopes. (1999) (6)
- Fast alignment of DNA and protein sequences. (1990) (6)
- Coarse-grained representation of β-helical protein building blocks (2007) (6)
- Studies of frequently recurring substructures in human alpha-like globin mRNA precursors. (1987) (6)
- Folding of two large nucleotide chains. (1984) (6)
- Computational validation of protein nanotubes. (2009) (6)
- 1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue. (2008) (6)
- Structural similarity of genetically interacting proteins (2008) (6)
- The mechanism of Raf activation through dimerization (2021) (5)
- Testing β-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids : A molecular dynamics study (2007) (5)
- Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data (2023) (5)
- Defective TRAF3 modulates alternative NF-kB signaling and cytokine expression to promote cancer cell survival in HPV positive head and neck cancer (TUM10P.1049) (2015) (5)
- An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences. (1987) (5)
- Deep generative molecular design reshapes drug discovery (2022) (5)
- Nearest Neighbor Nucleotide Patterns (2001) (5)
- Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies. (2018) (5)
- Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein. (2015) (5)
- Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease. (2021) (5)
- Geometrical docking algorithms. A practical approach. (2000) (5)
- The structural basis of Akt PH domain interaction with calmodulin (2021) (5)
- Identification of the intrinsic conformational properties of 1-aminocyclobutane-1-carboxylic acid (2006) (5)
- Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework (2022) (5)
- An interactive dot matrix system for locating potentially significant features in nucleic acid molecules. (1987) (5)
- Protein folding: lessons learned and new frontiers (2009) (5)
- Structural and combinatorial constraints on base pairing in large nucleotide sequences. (1984) (5)
- The ordering of nucleotides in the DNA: strong pyrimidine-purine patterns near homooligomer tracts. (1991) (5)
- A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly (2006) (5)
- A network-based deep learning methodology for stratification of tumor mutations (2021) (5)
- Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers (2019) (4)
- Neurodevelopmental disorders, immunity, and cancer are connected (2022) (4)
- Protein?protein interactions: principles and predictions (2005) (4)
- How can computation advance microbiome research? (2017) (4)
- Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment. (2008) (4)
- Efficient computational algorithms for docking and for generating and matching a library of functional epitopes I. Rigid and flexible hinge-bending docking algorithms. (1999) (4)
- Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA. (1989) (4)
- Probing Oligomerized Conformations of Defensin in the Membrane. (2017) (4)
- Conformational Profile of a Proline-Arginine Hybrid (2010) (4)
- Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era (2014) (4)
- Host-pathogen protein-nucleic acid interactions: A comprehensive review (2022) (4)
- Bioinformatics Study of Cancer-Related Mutations within p53 Phosphorylation Site Motifs (2014) (4)
- Transient, highly populated, building blocks folding model (2007) (4)
- Allostery modulates the beat rate of a cardiac pacemaker (2017) (4)
- Conserved putative signals in 3' intron junctions in rodents. (1987) (4)
- Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information. (2017) (4)
- The dynamic nature of the K-Ras/calmodulin complex can be altered by oncogenic mutations. (2021) (4)
- Computational Investigation of Gantenerumab and Crenezumab's Recognition of Aβ Fibrils in Alzheimer's Disease Brain Tissue. (2020) (4)
- Multiple Docking for Protein Structure Prediction (2005) (4)
- Alzheimer Aβ amyloid tubular fibrils: Insight into polymorphism (2011) (4)
- Potential folding–function interrelationship in proteins (2004) (4)
- Techniques for searching for structural similarities between protein cores, protein surfaces and between protein-protein interfaces (1996) (4)
- Computing the Dynamic Supramolecular Structural Proteome (2017) (4)
- Allosteric regulation of autoinhibition and activation of c-Abl (2022) (3)
- Dancing with Strings: The Conformational Dynamics of VQIXXK Motifs within Tau Protein in Monomer, Fibril and Hyper-Phosphorylated Filament States (2016) (3)
- Coarse-grained representation of beta-helical protein building blocks. (2007) (3)
- The structural basis of BCR-ABL recruitment of GRB2 in chronic myelogenous leukemia. (2022) (3)
- Tandem Domains with Tuned Interactions Are a Powerful Biological Design Principle (2015) (3)
- Eukaryotic oligomer frequencies are correlated with certain DNA helical parameters. (1985) (3)
- A hierarchical protein folding scheme based on the building block folding model. (2007) (3)
- Asymmetry in the distributions of the four nucleotides at mRNA initiation and 3' termini sites: some geometrical implications. (1987) (3)
- From computer vision to protein structure and association (1998) (3)
- Probing Structural Features of Alzheimer's β-Amyloid Ion Channels in Membranes Using Aβ Mutants (2011) (3)
- Bacteriophage lambda int protein may recognize structural features of the attachment sites. (1986) (3)
- Mechanistic Differences of Activation of Rac1P29S and Rac1A159V (2021) (3)
- Homology modeling and molecular dynamics simulations of lymphotactin (2000) (3)
- A deep learning framework for elucidating whole-genome chemical interaction space (2020) (3)
- Oncogenic K-Ras4B dimerization enhances downstream MAPK signaling. (2020) (3)
- Conformational Dynamics Allows Sampling of an "Active-like" State by Oncogenic K-Ras-GDP. (2022) (3)
- A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features (1988) (3)
- Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations. (2016) (3)
- Accurate prediction of molecular targets using a self-supervised image representation learning framework (2022) (3)
- Principles of Protein Recognition and Properties of Protein-protein Interfaces (2008) (3)
- Protein structure prediction using a docking‐based hierarchical folding scheme (2011) (3)
- Efficient algorithms for searching for exact repetition of nucleotide sequences (2005) (3)
- Survivin Expression Is Differentially Regulated by a Selective Cross-talk between RBM38 and miRNAs let-7b or miR-203a (2021) (3)
- The eukaryotic CCAAT and TATA boxes, DNA spacer flexibility and looping. (1992) (3)
- IKKα-deficient lung adenocarcinomas generate an immunosuppressive microenvironment by overproducing Treg-inducing cytokines (2022) (3)
- A New View of Activating Mutations in Cancer (2022) (3)
- Protein folding and function (2001) (2)
- Predicting Molecular Interactions in Structural Proteomics (2009) (2)
- Signaling in the crowded cell. (2021) (2)
- The structural basis of the oncogenic mutant K-Ras4B homodimers (2020) (2)
- Antigen Induced Dynamic Conformation Changes of Antibody to Facilitate Recognition of Fc Receptors (2018) (2)
- How Can PLOS Computational Biology Help the Biological Sciences? (2013) (2)
- Multiscale allostery: basic mechanisms and versatility in diagnostics and drug design. (2022) (2)
- Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK (2023) (2)
- Editorial overview: Folding and binding: Dynamic conformational heterogeneity is pivotal to cell life. (2016) (2)
- MIMTool: A Tool for Drawing Molecular Interaction Maps (2014) (2)
- The distributions of nucleotides near bacterial transcription initiation and termination sites show distinct signals that may affect DNA geometry (2005) (2)
- The Role of Allostery in the Termination of Second Messenger Signaling. (2015) (2)
- Conservation of polar residues at protein interfaces. (2000) (2)
- Studies of local stability in histone, U-snRNA and globin precursor mRNAs around transcription termination sites (1990) (2)
- The Allosteric Effect in Antibody-Antigen Recognition. (2020) (2)
- Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP (2012) (2)
- Simulation of the Distribution of Disordered Tau Proteins Around Its Amyloid Fibrils Core (2015) (2)
- What can we learn from highly connected beta-rich structures for structural interface design? (2008) (2)
- The predicted presence of large helical structural variation in yeast HIS4 upstream region is correlated with general amino acid control on the CYC1 gene. (1985) (2)
- MS2 RNA has a potential to form an unusually large number of stable hairpins. (1980) (2)
- Structure–Function Studies of Amyloid Pores in Alzheimer’s Disease as a Case Example of Neurodegenerative Diseases (2014) (2)
- The mechanism of activation of MEK1 by B-Raf and KSR1 (2022) (2)
- Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data Reveal their Clinical Impact (2021) (2)
- Conformational Ensemble of TteAdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition. (2021) (2)
- The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology (2016) (2)
- Intrinsic protein disorder in oncogenic KRAS signaling (2017) (2)
- Prediction of Protein Interaction Sites (2009) (2)
- Web interface for 3D visualization and analysis of SARS-CoV-2—human mimicry and interactions (2021) (2)
- DNA sequences at and between the GC and TATA boxes: potential DNA looping and spatial juxtapositioning of the protein factors. (1992) (2)
- Putative elements in the vicinity of viral transcription initiation sites. (1988) (2)
- A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. (2017) (2)
- Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity. (2017) (2)
- How PTEN mutations degrade function at the membrane and life expectancy of carriers of mutations in the human brain (2023) (2)
- RNA folding is unaffected by the nonrandom degenerate codon choice. (1982) (2)
- Sequence Context of Homooligomer Tracts in Eukaryotic Genomes: Some DNA Conformational Implications (1988) (2)
- Transmembrane β-Barrel Topology Model for Alzheimer's β-Amyloid (Aβ) Ion Channels (2011) (1)
- Real-Time Afm Imaging of Surface-Induced Oligomerization of the Non-Amyloidogenic P3 Peptide: Implications for Membrane Insertion and Ion Channel Formation (2010) (1)
- Splicing and transport of eukaryotic mRNAs: a theoretical model. (1982) (1)
- Rearrangements and Expansion of the Domain Content in Proteins Frequently Increase the Protein Connectivity in the Protein–Protein Interaction Network (2009) (1)
- Amylin–A b oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer’s disease † oligomerization. A recent study applied electrospray ionization-ion mobility spectroscopy-mass (2016) (1)
- Conformational Preferences of β – and γ –Aminated Proline Analogues (2010) (1)
- Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers. (2011) (1)
- Author Correction: In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor (2019) (1)
- PLOS Computational Biology 2017 Reviewer and Editorial Board Thank You (2018) (1)
- The structural network of Interleukin-10 and its implications in inflammation and cancer (2014) (1)
- Protein dynamics and conformational selection in bidirectional signal transduction (2012) (1)
- Activation of orphan receptor GPR132 induces cell differentiation in acute myeloid leukemia (2022) (1)
- Compilation and Analysis of Enzymes, Engineered Antibodies, and Nanoparticles Designed to Interfere with Amyloid‐β Aggregation (2017) (1)
- How to Write a Presubmission Inquiry (2015) (1)
- Critical building blocks in proteins: A common theme for folding and function (2002) (1)
- ChengF-Lab/mutanome v1.1 (2021) (1)
- HMI-PRED 2.0: a biologist-oriented web application for prediction of host–microbe protein–protein interaction by interface mimicry (2022) (1)
- Genome-wide transcription factor activities are explained by intrinsic conformational dynamics of binding-sites and distal flanking-regions (2015) (1)
- The Association of Protein–Protein Complexes (2009) (1)
- Effects of secondary structures in RNA on interlocking probabilities (1984) (1)
- Amylin–Ab oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer’s disease† (2016) (1)
- Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody (2022) (1)
- Title Amyloid beta Ion Channels in a Membrane Comprising Brain Total Lipid Extracts Permalink (2017) (1)
- AlphaFold, allosteric, and orthosteric drug discovery: Ways forward. (2023) (1)
- How has artificial intelligence impacted COVID-19 drug repurposing and what lessons have we learned? (2022) (1)
- The Association of Protein–Protein Complexes (2009) (1)
- Predictive modeling of moonlighting DNA-binding proteins (2022) (1)
- Genome-wide Prediction of Small Molecule Binding to Remote Orphan Proteins Using Distilled Sequence Alignment Embedding (2020) (1)
- Editorial overview: Catalysis and regulation: The beating heart of biology. (2021) (1)
- Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences (1991) (1)
- Probing the role of allostery in Rho and Ras GTPases (2017) (1)
- Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics (2021) (1)
- Coarse-graining the self-assembly of beta-helical protein building blocks. (2007) (1)
- Docking of protein molecules (1994) (1)
- Abstract 2310: Molecular dynamics simulation of permeation pathway of cytochrome C through Bax pore (2017) (1)
- Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family (2021) (1)
- Computational Approaches and Tools for Establishing Structural Models for Short Amyloid‐forming Peptides (2008) (1)
- Faculty Opinions recommendation of The RAS-ERK pathway: A route for couples. (2018) (1)
- Light-Induced Permeability Changes in Liposomes Containing Photo-Polymerizable Phospholipids (2010) (1)
- I-107 Long-range allosteric effects induced by Tax–HLA-A2 binding to an anti-HTLV-1 TCR: Implications for early T cell signaling (2019) (0)
- Structural features are as important as sequence homologies inDrosophila heat shock gene upstream regions (2005) (0)
- Higher‐order interactions of Bcr‐Abl can broaden chronic myeloid leukemia (CML) drug repertoire (2022) (0)
- CCDC 676504: Experimental Crystal Structure Determination (2009) (0)
- All D-Amino Acids Amyloid β Forms Ion Channels in Lipid Bilayers and is Toxic to Cells (2012) (0)
- Faculty Opinions recommendation of Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many. (2018) (0)
- Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics study. (2007) (0)
- New Methods Section in PLOS Computational Biology (2013) (0)
- Trends in the 5' vs. 3' flanks of oligonucleotides in eukaryotic and prokaryotic genomes: the asymmetric roles played by cytosine and guanine. (1991) (0)
- Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol) (2016) (0)
- Basic Principles of Protein–Protein Interaction (2009) (0)
- Modeling amyloid toxic ion channels (2009) (0)
- Low-Resolution Recognition Factors Determine Major Characteristics of the Energy Landscape in Protein–Protein Interaction (2009) (0)
- Abstract 2301: Atomic-level insights into PI3K activation (2021) (0)
- Allosteric Effects and Signal Transduction in the Peptide-MHC Binding to a Human T Cell Receptor (2019) (0)
- Ras Signaling: Allostery, Conformation, and Function (2018) (0)
- New Methods Section in. (2013) (0)
- Integrating the intrinsic conformational preferences of non-coded α-amino acids modified at the peptide bond into the NCAD database (2011) (0)
- Searching For the Hinge of E3 Ubiquitin Ligase Machinery with MD Simulations (2009) (0)
- Close-Range Electrostatic Interactions in Proteins. (2002) (0)
- Computing Biology (2016) (0)
- Prediction of Protein-Protein Interactions at Genome Scale (2011) (0)
- Nanostructure design: methods and protocols. Preface. (2008) (0)
- Combining Protein-protein Interaction Networks with Structures (2009) (0)
- Protein–Protein Docking (2009) (0)
- Abstract PR04: A bimodal mechanism of RAS inactivation by monoubiquitination (2023) (0)
- Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6 (2016) (0)
- Abstract 2457: Mechanisms of membrane binding of K-Ras4B farnesylated hypervariable region (2015) (0)
- Modeling Ion-Permeable β-Amyloid (Aβ) Barrels in the Lipid Bilayer (2010) (0)
- Small GTPase Ran: Depicting the nucleotide-specific conformational landscape of the functionally important C-terminus (2023) (0)
- Comprar Nanostructure Design · Methods and Protocols | Gazit, Ehud | 9781934115350 | Springer (2008) (0)
- PCCP--a society journal going from strength to strength. (2015) (0)
- In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor (2017) (0)
- Exploring the Aggregation Mechanism of Intrinsically Disordered Tau Protein (2017) (0)
- Abstract 872: Deciphering the activation mechanism of CDK4/cyclin-D complex that differs from the CDK2/cyclin-E complex (2023) (0)
- P53-Response Element Complex Organization is Dominated by Lys120 Interactions with Variant Nucleotides (2011) (0)
- Elucidating the Functional Significance of the C-Terminal Hypervariable Region (HVR) in K-Ras4A (2015) (0)
- 1 Pharmacophore Detection by Multiple Flexible Alignment of Drug-Like Molecules (2007) (0)
- Visualizing RNA conformational and architectural heterogeneity in solution (2023) (0)
- Crystal Structure of human Ubc9 (K48A/K49A/E54A) (2016) (0)
- Modeling Transmembrane β‐Amyloid (Aβ) Barrels of Alzheimer's Ion Channels (2011) (0)
- Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole) (2016) (0)
- Principles of allosteric mechanisms in cell signaling (2015) (0)
- Long-range effects induced by peptide-MHC binding to a human T cell receptor: Implications for the initiation of T cell signaling (2018) (0)
- Abstract 3224: High affinity interaction of K-Ras4B hypervariable region with Ras active site (2014) (0)
- Mapping Protein Function by Combinatorial Mutagenesis (2009) (0)
- Abstract 2085: Structural principles of kinase-selectivity drug design (2023) (0)
- Data‐driven model of the KRas4B/Calmodulin complex (2021) (0)
- Abstract 1111: Altered inflammatory and death pathways in head and neck cell lines model genomic and expression signatures identified in The Cancer Genome Atlas (2015) (0)
- Abstract 678: Raf-1 cysteine-rich domain (CRD) supports active orientations of KRas4B/Raf-1 at the membrane (2018) (0)
- Intrinsic conformational characteristics of alpha,alpha-diphenylglycine. (2007) (0)
- Basic Principles of Protein–Protein Interaction (2009) (0)
- Faculty Opinions recommendation of Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM. (2019) (0)
- Abstract 81: RNA-seq, exome-seq, functional RNAi screening and bioinformatics analyses identify molecules promoting aberrant activation of classical and alternative NF-kB pathways in head and neck cell lines (2016) (0)
- Long range and symmetry considerations in the DNA. (1991) (0)
- Allosteric effects and regulation of signaling: the ubiquitin E3 ligases (2009) (0)
- Abstract 2918: Comprehensive survey of KRas4B membrane interaction and orientation (2022) (0)
- Probing the Stability of Fibril and Tubular Species Using All-Atom Molecular Dynamics Simulations in Solution: Insight into Polymorphism (2013) (0)
- Inside front cover. (2016) (0)
- Abstract 683: SOS1 allosterically linked conformational changes modulate KRas4B activation (2018) (0)
- Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane (2017) (0)
- P53 Induced Dna Bending (2009) (0)
- Toxic $\beta $-Amyloid (A$\beta )$ Alzheimer's Ion Channels: From Structure to Function and Design (2012) (0)
- Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146) (2016) (0)
- [Invited Lecture] Structural motifs in the interior and on the surfaces of protein monomers and at protein-protein interfaces (1998) (0)
- The mechanism of activation of MEK1 by B-Raf and KSR1 (2022) (0)
- Abstract 2270: Membrane organization of KRas4B with regulatory domain of Raf-1 (2021) (0)
- Strong sequence patterns in eukaryotic promoter regions: potential implications for DNA structure. (1993) (0)
- Protegrin-1 (PG-1), An Antimicrobial Peptide Forms Ion Channels: Atomic Force Microscopy, Channel Conductance, and Molecular Dynamics Simulation Study (2010) (0)
- CCDC 676502: Experimental Crystal Structure Determination (2009) (0)
- Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from fragment cocktail screen) (2016) (0)
- Structural wrinkles and the genomic regulatory sites of eukaryotes (2005) (0)
- Molecular dynamics simulations reveal distinct conformational changes of three cullins in cullin‐RING E3 ubiquitin ligases (2011) (0)
- Flowchart summary of the prediction algorithm (2011) (0)
- My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype (2021) (0)
- Abstract 148: New conformational details help in clarifying Raf activation by dimerization (2022) (0)
- Designing Protein–Protein Interaction Inhibitors (2009) (0)
- Principles of Shape‐Driven Nanostructure Design via Self‐Assembly of Protein Building Blocks (2013) (0)
- Author Correction: In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor (2019) (0)
- The Evolution of the Natively Disordered Region in P53 Family Proteins (2011) (0)
- A Review of 2011 for PLoS Computational Biology (2012) (0)
- Hydrophobic Interactions and Biomolecular Binding Versus Folding (2003) (0)
- Strategy toward Kinase-Selective Drug Discovery (2023) (0)
- fragment folding and assembly Reducing the computational complexity of protein folding via (2002) (0)
- Abstract 2919: The structural basis of BCR-ABL recruitment of GRB2 in chronic myelogenous leukemia (2022) (0)
- CCDC 676505: Experimental Crystal Structure Determination (2009) (0)
- Abstract 1367: The dynamic mechanism of SARAH domain in RASSF5 activation by K-Ras4B (2017) (0)
- Abstract 3435: Genome-wide RNA and DNA high throughput sequencing reveals proinflammatory and death gene signatures in head and neck squamous cell carcinoma lines with different HPV status (2014) (0)
- Abstract 3170: Alternative NF-κB pathway activation enhanced by deficient TRAF3 in human papillomavirus (HPV)-associated head and neck cancer (2014) (0)
- CCDC 676503: Experimental Crystal Structure Determination (2009) (0)
- Abstract 2678: Novel host-pathogen interactions of Helicobacter pylori and their implications to gastric cancer (2017) (0)
- Intrinsic Conformational Preferences of C α , α -Dibenzylglycine (2009) (0)
- Faculty Opinions recommendation of Structural basis of the atypical activation mechanism of KRASV14I. (2019) (0)
- Cooperativities Among Short Amyloid Stretches Within Long Amyloidogenic Sequence Segment (2012) (0)
- Interactions: Induced Fit (2001) (0)
- Development of ultra-high affinity bivalent ligands targeting the polo-like kinase 1 (2022) (0)
- Faculty Opinions recommendation of Tissue-specificity in cancer: The rule, not the exception. (2019) (0)
- 1P257 Clusters of conserved residue in DNA-binding proteins : Analogy with hot spots and implications to prediction(Bioinformatics-structural, functional, and comparative genomics,Oral Presentations) (2007) (0)
- Alzheimer's β-Amyloid All-D-Enantiomers and Native All-L-Enantiomers Exhibit Similar Pore Structures in Lipid Bilayers: Atomic Force Microscopy (2012) (0)
- Abstract 682: The mechanism of PI3Kα activation by SH2 release (2018) (0)
- Faculty Opinions recommendation of Distinct Binding Preferences between Ras and Raf Family Members and the Impact on Oncogenic Ras Signaling. (2019) (0)
- Computational Simulations of Protein– Protein and Protein– Nucleic Acid Association (2009) (0)
- Bio-geometry: challenges, approaches, and future opportunities in proteomics and drug discovery (2008) (0)
- Abstract 873: The mechanisms of SHP2 activation in cancer and neurodevelopmental disorder (2023) (0)
- Energy Centrality Relationship Reduces False Positive Prediction in Protein Docking (2013) (0)
- Faculty Opinions recommendation of M-Ras/Shoc2 signaling modulates E-cadherin turnover and cell-cell adhesion during collective cell migration. (2019) (0)
- Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences (2017) (0)
- Sequence‐Dependent Specific p53‐Response Element Interactions Direct P53 organization and Control Transcription Selectivity (2011) (0)
- Faculty Opinions recommendation of Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability. (2018) (0)
- Polymorphism in Alzheimer Aβ Amyloid Organization: Insight into Aβ Aggregation (2010) (0)
- Modeling Protein Assemblies in the Proteome* S (2014) (0)
- Modeling Variants of Alzheimer's Ion Channels in the Lipid Bilayer formed by an Aggregation-Intermediate β-Hairpin and E22Δ Mutant (2013) (0)
- Self-assembly of fused homo-oligomers to create nanotubes. (2008) (0)
- Abstract 5145: A new discovering motif on SOS1 PR domain clues Grb2-SOS1 association (2019) (0)
- Precision medicine review: rare driver mutations and their biophysical classification (2019) (0)
- Faculty Opinions recommendation of BAR domain proteins-a linkage between cellular membranes, signaling pathways, and the actin cytoskeleton. (2018) (0)
- Identification of Druggable Hot Spots on Proteins and in Protein– Protein Interfaces (2009) (0)
- Conformational Control of Ubiquitination in the Cullin-Ring E3 Ligase Machinery (2010) (0)
- The (still) underappreciated role of allostery in the cellular network (2019) (0)
- Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention (2018) (0)
- CCDC 676501: Experimental Crystal Structure Determination (2009) (0)
- The Mechanism of Full Activation of Tumor Suppressor PTEN at the Phosphatidylinositol-Enriched Membrane (2021) (0)
- The origin of Allosteric Modulation: Multiple Pre-existing Pathways Selection (2009) (0)
- Nonrandom recurrence of consecutive repeats in noncoding mammalian sequences (1986) (0)
- 62 a Sunday , February 8 , 2015 Intrinsically Disordered Proteins ( IDP ) and Aggregates (2015) (0)
- Large Scale Prediction of Computational Hot Spots in Protein Interfaces (2009) (0)
- Pan-cancer clinical impact of latent drivers from double mutations (2023) (0)
- Faculty Opinions recommendation of Biochemical Characterization of Intact Oncogenic BRAFV600E Together With Molecular Dynamics Simulations Provide Insight into the Activation and Inhibition Mechanisms of RAF Kinases. (2019) (0)
- Faculty Opinions recommendation of Bifunctional Small-Molecule Ligands of K-Ras Induce Its Association with Immunophilin Proteins. (2019) (0)
- Abstract 2763: Raf-1 cysteine-rich domain (CRD) promotes active KRas4B membrane orientation facilitating dimerization through the allosteric lobe interface (2019) (0)
- A new network attack strategy mimicking drug mechanism: Interface attack (2011) (0)
- Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions (2023) (0)
- Comprehensive characterization of multi-omic landscapes between gut-microbiota metabolites and the G-protein-coupled receptors in Alzheimer’s disease (2022) (0)
- GPR132 Has Therapeutic Efficacy in Acute Myeloid Leukemia in Vivo by Promoting Cellular Differentiation in an mTOR Dependent Way: Identification of 8-Gingerol as a Novel Agonist (2022) (0)
- 42-Residue Beta Amyloid Fibril (2015) (0)
- Modeling Alzheimer's Ion Channel Structures in Lipid Bilayers Formed by D- and L-Enantiomers of Beta-Amyloid (1-42) Peptide (2012) (0)
- Correction to Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils. (2018) (0)
- Intrinsically Disordered Proteins and Their Recognition Functions (2009) (0)
- Abstract 1500: How K-Ras4B attaches to the membrane and forms a dimer: A new paradigm (2016) (0)
- Folding and binding cascades: Shift (2017) (0)
- Polymophism of A-Beta1-42 Peptide Oligomer - Membrane Interactions (2010) (0)
- Activation mechanisms of clinically distinct B‐Raf V600E and V600K mutants (2022) (0)
- Raf-1 Cysteine-Rich Domain (CRD) Promotes Active Orientation and Dimerization of KRas4B at the Membrane (2019) (0)
- Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen) (2016) (0)
- Ras Isoforms Conformational Clustering and Community Networks Studies: Simulating Ras with Accelerated Molecular Dynamics (2015) (0)
- Autobiography of Ruth Nussinov. (2021) (0)
- Membrane binding of HVR KRas 4 B 1 Mechanisms of Membrane Binding of Small GTPase KRas 4 B Farnesylated Hypervariable Region * (2015) (0)
- Abstract 5229: High affinity interaction of K-Ras4B HVR with calmodulin (2017) (0)
- A Future Vision for PLOS Computational Biology (2012) (0)
- A Review of 2010 for PLoS Computational Biology (2011) (0)
- Structure Based Search for Multiple Binding Sites of SOS1 PR Domain Recognizes an Uncovered Motif Favoring GRB2-SOS1 Association (2019) (0)
- Computational Study of Cytolytic Peptides: Monomeric-Oligomeric Structures and Ligand Interactions (2005) (0)
- Neurodevelopmental disorders and cancer networks share pathways; but differ in mechanisms, signaling strength, and outcome (2023) (0)
- Faculty Opinions recommendation of Akt kinase activation mechanisms revealed using protein semisynthesis. (2019) (0)
- DNA spatial considerations in the arrangement of G/C and A/T blocks. (1992) (0)
- RAS Signaling in the PI3K/AKT/MTOR Pathway (2020) (0)
- Prediction of Novel Host-Pathogen Interactions for Helicobacter Pylori Through Interface Mimicry and their Implications to Gastric Cancer (2019) (0)
- Nucleotide-Dependent Membrane Interaction and Dimerization of K-Ras4B (2015) (0)
- Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family (2021) (0)
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What Schools Are Affiliated With Ruth Nussinov?
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