Published in Mol Cell on January 01, 2002
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res (2004) 4.30
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J (2003) 2.91
OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res (2011) 2.28
Membrane binding domains. Biochim Biophys Acta (2006) 1.67
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res (2008) 1.61
Specific translocation of protein kinase Calpha to the plasma membrane requires both Ca2+ and PIP2 recognition by its C2 domain. Mol Biol Cell (2005) 1.47
Mechanism of specific membrane targeting by C2 domains: localized pools of target lipids enhance Ca2+ affinity. Biochemistry (2007) 1.42
Phosphatidylserine targeting for diagnosis and treatment of human diseases. Apoptosis (2010) 1.42
C2 domain of protein kinase C alpha: elucidation of the membrane docking surface by site-directed fluorescence and spin labeling. Biochemistry (2003) 1.40
C2 domains of protein kinase C isoforms alpha, beta, and gamma: activation parameters and calcium stoichiometries of the membrane-bound state. Biochemistry (2002) 1.39
Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys J (2004) 1.38
Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem (2005) 1.37
Investigating lipid composition effects on the mechanosensitive channel of large conductance (MscL) using molecular dynamics simulations. Biophys J (2003) 1.36
Single molecule diffusion of membrane-bound proteins: window into lipid contacts and bilayer dynamics. Biophys J (2010) 1.35
Synaptotagmin C2A loop 2 mediates Ca2+-dependent SNARE interactions essential for Ca2+-triggered vesicle exocytosis. Mol Biol Cell (2007) 1.32
A computational model for the electrostatic sequestration of PI(4,5)P2 by membrane-adsorbed basic peptides. Biophys J (2004) 1.32
Membrane-docking loops of the cPLA2 C2 domain: detailed structural analysis of the protein-membrane interface via site-directed spin-labeling. Biochemistry (2003) 1.28
Biochemical characterization of rous sarcoma virus MA protein interaction with membranes. J Virol (2005) 1.27
Structural genomics: computational methods for structure analysis. Protein Sci (2003) 1.24
Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains. Annu Rev Biophys Biomol Struct (2005) 1.23
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23
The role of hydrophobic interactions in positioning of peripheral proteins in membranes. BMC Struct Biol (2007) 1.20
Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Model Simul (2006) 1.19
Self-induced docking site of a deeply embedded peripheral membrane protein. Biophys J (2006) 1.14
Increased concentration of polyvalent phospholipids in the adsorption domain of a charged protein. Biophys J (2004) 1.14
X-ray reflectivity studies of cPLA2{alpha}-C2 domains adsorbed onto Langmuir monolayers of SOPC. Biophys J (2005) 1.11
Formin homology 2 domains occur in multiple contexts in angiosperms. BMC Genomics (2004) 1.11
Protein kinase C-induced phosphorylation of Orai1 regulates the intracellular Ca2+ level via the store-operated Ca2+ channel. J Biol Chem (2010) 1.09
Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites. BMC Struct Biol (2008) 1.09
Cytotoxic ribonucleases: the dichotomy of Coulombic forces. Biochemistry (2007) 1.09
Molecular modeling of the membrane targeting of phospholipase C pleckstrin homology domains. Protein Sci (2003) 1.08
Fast endocytosis is inhibited by GABA-mediated chloride influx at a presynaptic terminal. Neuron (2004) 1.07
Effect of PIP2 binding on the membrane docking geometry of PKC alpha C2 domain: an EPR site-directed spin-labeling and relaxation study. Biochemistry (2008) 1.07
Phosphatidylinositol 4,5-bisphosphate alters synaptotagmin 1 membrane docking and drives opposing bilayers closer together. Biochemistry (2011) 1.06
Molecular dynamics simulations of PIP2 and PIP3 in lipid bilayers: determination of ring orientation, and the effects of surface roughness on a Poisson-Boltzmann description. Biophys J (2009) 1.05
The calcium-dependent and calcium-independent membrane binding of synaptotagmin 1: two modes of C2B binding. J Mol Biol (2009) 1.05
Ca2+ regulation in the Na+/Ca2+ exchanger features a dual electrostatic switch mechanism. Proc Natl Acad Sci U S A (2009) 1.05
Localization and function of cytosolic phospholipase A2alpha at the Golgi. Biochimie (2010) 1.01
Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer. Biochemistry (2005) 1.01
Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. J Biol Chem (2008) 0.99
Calcium binding by synaptotagmin's C2A domain is an essential element of the electrostatic switch that triggers synchronous synaptic transmission. J Neurosci (2012) 0.99
Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc (2009) 0.98
The calcium binding loops of the cytosolic phospholipase A2 C2 domain specify targeting to Golgi and ER in live cells. Mol Biol Cell (2003) 0.97
Defining the membrane-associated state of the PTEN tumor suppressor protein. Biophys J (2013) 0.92
Physical determinants of β-barrel membrane protein folding in lipid vesicles. Biophys J (2011) 0.90
Cellular and molecular interactions of phosphoinositides and peripheral proteins. Chem Phys Lipids (2014) 0.89
The C2 domains of otoferlin, dysferlin, and myoferlin alter the packing of lipid bilayers. Biochemistry (2013) 0.89
Pb2+ as modulator of protein-membrane interactions. J Am Chem Soc (2011) 0.89
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold. Proteins (2006) 0.89
Separate membrane targeting and anchoring domains function in the localization of the S. cerevisiae Cdc24p guanine nucleotide exchange factor. Curr Genet (2004) 0.87
Configuration of PKCalpha-C2 domain bound to mixed SOPC/SOPS lipid monolayers. Biophys J (2009) 0.87
Ca2+ activation of the cPLA2 C2 domain: ordered binding of two Ca2+ ions with positive cooperativity. Biochemistry (2004) 0.86
Phosphatidylserine in the brain: metabolism and function. Prog Lipid Res (2014) 0.85
C2 domain protein MIN1 promotes eyespot organization in Chlamydomonas reinhardtii. Eukaryot Cell (2008) 0.85
The cooperative response of synaptotagmin I C2A. A hypothesis for a Ca2+-driven molecular hammer. Biophys J (2006) 0.84
Electrostatic and hydrophobic interactions differentially tune membrane binding kinetics of the C2 domain of protein kinase Cα. J Biol Chem (2013) 0.83
Hydrophobic contributions to the membrane docking of synaptotagmin 7 C2A domain: mechanistic contrast between isoforms 1 and 7. Biochemistry (2012) 0.82
Dynamics and Membrane Interactions of Protein Kinase C. Biochemistry (2015) 0.82
The cPLA2 C2alpha domain in solution: structure and dynamics of its Ca2+-activated and cation-free states. Biophys J (2006) 0.81
The molecular basis of ceramide-1-phosphate recognition by C2 domains. J Lipid Res (2012) 0.81
C2 domain membrane penetration by group IVA cytosolic phospholipase A₂ induces membrane curvature changes. J Lipid Res (2012) 0.81
Interactions of the auxilin-1 PTEN-like domain with model membranes result in nanoclustering of phosphatidyl inositol phosphates. Biophys J (2013) 0.81
An electrostatically preferred lateral orientation of SNARE complex suggests novel mechanisms for driving membrane fusion. PLoS One (2010) 0.79
Anoctamins/TMEM16 Proteins: Chloride Channels Flirting with Lipids and Extracellular Vesicles. Annu Rev Physiol (2016) 0.78
Mutations that disrupt Ca²⁺-binding activity endow Doc2β with novel functional properties during synaptic transmission. Mol Biol Cell (2013) 0.78
Phosphatidylinositol-4,5-bisphosphate enhances anionic lipid demixing by the C2 domain of PKCα. PLoS One (2014) 0.77
PTEN-Associated Complexes: An Overview. Curr Top Biochem Res (2010) 0.77
Self-consistent description of electrokinetic phenomena in particle-based simulations. J Chem Phys (2015) 0.77
Cd2+ as a Ca2+ surrogate in protein-membrane interactions: isostructural but not isofunctional. J Am Chem Soc (2013) 0.77
The C2 domains of granuphilin are high-affinity sensors for plasma membrane lipids. Chem Phys Lipids (2013) 0.76
VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials. PLoS Comput Biol (2014) 0.76
A phosphorylation switch controls the spatiotemporal activation of Rho GTPases in directional cell migration. Nat Commun (2015) 0.76
Synergistic effect of Pb(2+) and phosphatidylinositol 4,5-bisphosphate on C2 domain-membrane interactions. Biochemistry (2012) 0.76
A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding. Biophys J (2016) 0.75
C2-domain mediated nano-cluster formation increases calcium signaling efficiency. Sci Rep (2016) 0.75
RAB-10 Promotes EHBP-1 Bridging of Filamentous Actin and Tubular Recycling Endosomes. PLoS Genet (2016) 0.75
Dynamic Response of the C2 Domain of Protein Kinase Cα to Ca(2+) Binding. Biophys J (2016) 0.75
Nuclear membrane stretch and its role in mechanotransduction. Nucleus (2017) 0.75
The role of DNA shape in protein-DNA recognition. Nature (2009) 5.52
A hierarchical approach to all-atom protein loop prediction. Proteins (2004) 5.18
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem (2002) 5.18
Origins of specificity in protein-DNA recognition. Annu Rev Biochem (2010) 4.43
GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol (2003) 3.58
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell (2011) 3.40
Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 3.37
Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell (2007) 3.34
Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci U S A (2002) 3.23
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins (2003) 3.04
Type II cadherin ectodomain structures: implications for classical cadherin specificity. Cell (2006) 2.85
On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol (2002) 2.73
Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol (2006) 2.37
Identification of a chloride ion binding site in Na+/Cl -dependent transporters. Proc Natl Acad Sci U S A (2007) 2.32
The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure (2011) 2.19
Protein structure prediction: inroads to biology. Mol Cell (2005) 2.08
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res (2003) 1.97
Cadherin-mediated cell-cell adhesion: sticking together as a family. Curr Opin Struct Biol (2003) 1.94
On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins (2006) 1.90
Loop modeling: Sampling, filtering, and scoring. Proteins (2008) 1.81
On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J (2006) 1.79
Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site. J Mol Biol (2004) 1.76
Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature (2011) 1.73
Thinking outside the cell: how cadherins drive adhesion. Trends Cell Biol (2012) 1.72
Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle. Structure (2005) 1.71
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol (2010) 1.70
Searching for neuronal left/right asymmetry: genomewide analysis of nematode receptor-type guanylyl cyclases. Genetics (2006) 1.68
Splice form dependence of beta-neurexin/neuroligin binding interactions. Neuron (2010) 1.68
Two-step adhesive binding by classical cadherins. Nat Struct Mol Biol (2010) 1.67
On the role of electrostatic interactions in the design of protein-protein interfaces. J Mol Biol (2002) 1.65
PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res (2012) 1.59
Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci U S A (2009) 1.54
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res (2007) 1.40
Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. J Mol Biol (2006) 1.39
T-cadherin structures reveal a novel adhesive binding mechanism. Nat Struct Mol Biol (2010) 1.37
A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol (2011) 1.35
On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol (2003) 1.34
Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. J Mol Biol (2009) 1.34
Nuance in the double-helix and its role in protein-DNA recognition. Curr Opin Struct Biol (2009) 1.32
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? J Mol Biol (2008) 1.31
Helical packing patterns in membrane and soluble proteins. Biophys J (2004) 1.30
An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans. Development (2006) 1.26
PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res (2011) 1.25
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity. J Mol Biol (2004) 1.24
Comparative study of generalized born models: Born radii and peptide folding. J Phys Chem B (2005) 1.24
Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. Structure (2008) 1.24
Structural genomics: computational methods for structure analysis. Protein Sci (2003) 1.24
Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol (2009) 1.23
Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering. Proteins (2006) 1.18
Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol (2011) 1.14
The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexes. J Mol Biol (2004) 1.10
Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J (2007) 1.10
Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn (2010) 1.08
Comparative study of generalized Born models: protein dynamics. Proc Natl Acad Sci U S A (2005) 1.08
Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4. Structure (2008) 1.07
The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J Struct Funct Genomics (2010) 1.07
An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins (2005) 1.07
Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions. Mol Cell (2012) 1.05
Nectin ectodomain structures reveal a canonical adhesive interface. Nat Struct Mol Biol (2012) 1.04
Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J Mol Biol (2010) 1.03
Prediction of side-chain conformations on protein surfaces. Proteins (2007) 1.03
Loop L5 acts as a conformational latch in the mitotic kinesin Eg5. J Biol Chem (2010) 1.02
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A (2007) 1.01
Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains. J Mol Biol (2003) 1.01
Local quality assessment in homology models using statistical potentials and support vector machines. Protein Sci (2007) 1.00
Lozenge directly activates argos and klumpfuss to regulate programmed cell death. Genes Dev (2005) 1.00
An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys J (2004) 1.00
Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. J Biol Chem (2008) 0.99
Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus. Proteins (2009) 0.97
Theory and simulations of adhesion receptor dimerization on membrane surfaces. Biophys J (2013) 0.97
Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca²+-free interdomain linkers. Proc Natl Acad Sci U S A (2011) 0.96
Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach. Proc Natl Acad Sci U S A (2011) 0.94
Structural bioinformatics of the interactome. Annu Rev Biophys (2014) 0.93
Protein structure space is much more than the sum of its folds. Nat Struct Mol Biol (2007) 0.93
Using systems and structure biology tools to dissect cellular phenotypes. J Am Med Inform Assoc (2011) 0.92
Biophysics: Flipping Watson and Crick. Nature (2011) 0.91
Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin. J Mol Biol (2011) 0.91
VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. PLoS Comput Biol (2010) 0.90
MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Res (2011) 0.89
Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold. Protein Sci (2003) 0.88
NMR structure of the 18 kDa protein CC1736 from Caulobacter crescentus identifies a member of the START domain superfamily and suggests residues mediating substrate specificity. Proteins (2005) 0.87
Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Proc Natl Acad Sci U S A (2008) 0.87
Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion. Proc Natl Acad Sci U S A (2013) 0.86
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res (2013) 0.85
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci (2003) 0.84
Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes. Protein Sci (2005) 0.83
Toward a "structural BLAST": using structural relationships to infer function. Protein Sci (2013) 0.83
NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif. Proteins (2007) 0.82
NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle. Proteins (2004) 0.82
Crystal structures of MTH1187 and its yeast ortholog YBL001c. Proteins (2003) 0.81
To B or not to B: PIP2 answers the question. Dev Cell (2005) 0.81
Bending in the right direction. Structure (2005) 0.80
Using structure to explore the sequence alignment space of remote homologs. PLoS Comput Biol (2011) 0.79
High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J Struct Funct Genomics (2010) 0.79
PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Res (2010) 0.79
NMR structure of protein PA2021 from Pseudomonas aeruginosa. Proteins (2006) 0.78
NMR structure of the hypothetical protein AQ-1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold. Proteins (2004) 0.77
VISTAL--a new 2D visualization tool of protein 3D structural alignments. Bioinformatics (2006) 0.77