The Ubiquitin Domain Superfold: Structure-based Sequence Alignments and Characterization of Binding Epitopes

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SMART, a simple modular architecture research tool: Identification of signaling domains

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The GTPase superfamily: conserved structure and molecular mechanism

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Mechanisms of type-I- and type-II-interferon-mediated signalling

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CATH – a hierarchic classification of protein domain structures

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The FoldX web server: an online force field

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The GTPase superfamily: a conserved switch for diverse cell functions

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Phosphatidylinositol-3-OH kinase direct target of Ras

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Structure of ubiquitin refined at 1.8 Å resolution

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Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations

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A Multiubiquitin Chain Is Confined to Specific Lysine in a Targeted Short-Lived Protein

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ERM proteins and merlin: integrators at the cell cortex

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How Proteolysis Drives the Cell Cycle

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Receptor downregulation and multivesicular-body sorting

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Regulation of Membrane Protein Transport by Ubiquitin and Ubiquitin-Binding Proteins

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Protein superfamilles and domain superfolds

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Structure of an HIF-1α-pVHL Complex: Hydroxyproline Recognition in Signaling

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Recent improvements to the SMART domain-based sequence annotation resource

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Ulp1-SUMO Crystal Structure and Genetic Analysis Reveal Conserved Interactions and a Regulatory Element Essential for Cell Growth in Yeast

2000 • 674 citations

The 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with RaplA and a GTP analogue

1995 • 627 citations

Crystal Structure of a UBP-Family Deubiquitinating Enzyme in Isolation and in Complex with Ubiquitin Aldehyde

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Crystal Structure and Functional Analysis of Ras Binding to Its Effector Phosphoinositide 3-Kinase γ

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Cortical Actin Organization: Lessons from ERM (Ezrin/Radixin/Moesin) Proteins

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Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

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Epsins and Vps27p/Hrs contain ubiquitin-binding domains that function in receptor endocytosis

2002 • 417 citations

Targeting of substrates to the 26S proteasome

1997 • 362 citations

Interrogating protein interaction networks through structural biology

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Prediction of water and metal binding sites and their affinities by using the Fold-X force field

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The Natural History of Protein Domains

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The activation of phosphatidylinositol 3-kinase by Ras

1994 • 322 citations

3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments

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Rational design of faster associating and tighter binding protein complexes.

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Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales

1994 • 294 citations

Structure and functional interactions of the Tsg101 UEV domain

2002 • 294 citations

Structural basis for the specificity of ubiquitin C-terminal hydrolases

1999 • 279 citations

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Cloning of the ALL-1 fusion partner, the AF-6 gene, involved in acute myeloid leukemias with the t(6;11) chromosome translocation.

1993 • 260 citations

The Structure of the APPBP1-UBA3-NEDD8-ATP Complex Reveals the Basis for Selective Ubiquitin-like Protein Activation by an E1

2003 • 260 citations

Structural basis for the interaction of Ras with RaIGDS

1998 • 251 citations

Ubiquitin interactions of NZF zinc fingers

2004 • 240 citations

Solution Structure of a CUE-Ubiquitin Complex Reveals a Conserved Mode of Ubiquitin Binding

2003 • 236 citations

Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p

2003 • 224 citations

Ubiquitin Recognition by the Human TSG101 Protein

2004 • 221 citations

Ras/Rap effector specificity determined by charge reversal

1996 • 214 citations

InterPreTS: protein <u>Inter</u>action <u>Pre</u>diction through <u>T</u>ertiary <u>S</u>tructure

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Identification of AF-6 and Canoe as Putative Targets for Ras

1996 • 207 citations

Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation

2003 • 205 citations

Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar 1 1Edited by B. Honig

1998 • 199 citations

Assigning genomic sequences to CATH

2000 • 192 citations

A Basis for SUMO Protease Specificity Provided by Analysis of Human Senp2 and a Senp2-SUMO Complex

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Entropy in biological binding processes: Estimation of translational entropy loss

1994 • 179 citations

Ras–effector interactions: after one decade

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Recognizing and Defining True Ras Binding Domains I: Biochemical Analysis

2005 • 175 citations

Structure of a Conjugating Enzyme-Ubiquitin Thiolester Intermediate Reveals a Novel Role for the Ubiquitin Tail

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Transient Kinetic Studies on the Interaction of Ras and the Ras-Binding Domain of c-Raf-1 Reveal Rapid Equilibration of the Complex

1998 • 129 citations

Multiple sequence alignments

2005 • 127 citations

Structural determinants for the binding of ubiquitin-like domains to the proteasome

2003 • 123 citations

Structural Insights into Endosomal Sorting Complex Required for Transport (ESCRT-I) Recognition of Ubiquitinated Proteins

2004 • 122 citations

RalGDS-like factor (Rlf) is a novel Ras and Rap 1A-associating protein.

1996 • 121 citations

New insights into the mechanism of protein–protein association

2001 • 113 citations

Recognizing and Defining True Ras Binding Domains II: In Silico Prediction Based on Homology Modelling and Energy Calculations

2005 • 110 citations

Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex

2004 • 108 citations

Structural and biochemical analysis of Ras‐effector signaling via RalGDS

1999 • 99 citations

A Detailed Thermodynamic Analysis of Ras/Effector Complex Interfaces

2004 • 89 citations

Protein complexes: structure prediction challenges for the 21st century

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Site-Directed Mutagenesis of Ubiquitin. Differential Roles for Arginine in the Interaction with Ubiquitin-Activating Enzyme

1994 • 86 citations

Structure of the Ubiquitin-interacting Motif of S5a Bound to the Ubiquitin-like Domain of HR23B

2004 • 83 citations

Local water bridges and protein conformational stability

1999 • 70 citations

Predicting Reliable Regions in Protein Alignments from Sequence Profiles

2003 • 61 citations

The Activation of RalGDS Can Be Achieved Independently of Its Ras Binding Domain

2002 • 49 citations

The binding site for UCH-L3 on ubiquitin: mutagenesis and NMR studies on the complex between ubiquitin and UCH-L3

1999 • 40 citations

Ras‐binding domains: predicting function versus folding

1997 • 39 citations

SQUARE—determining reliable regions in sequence alignments

2004 • 22 citations