Published in Nat Struct Mol Biol on June 01, 2007
Exploration of uncharted regions of the protein universe. PLoS Biol (2009) 3.41
Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers. Structure (2008) 1.52
Characterization of proteins with wide-angle X-ray solution scattering (WAXS). J Struct Funct Genomics (2010) 1.30
Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PLoS Comput Biol (2009) 1.14
Conservation of protein structure over four billion years. Structure (2013) 0.87
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
Electrostatic control of the membrane targeting of C2 domains. Mol Cell (2002) 2.18
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
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res (2011) 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
Prediction of side-chain conformations on protein surfaces. Proteins (2007) 1.03
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
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
An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys J (2004) 1.00
Lozenge directly activates argos and klumpfuss to regulate programmed cell death. Genes Dev (2005) 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
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 the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle. Proteins (2004) 0.82
NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif. Proteins (2007) 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
High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J Struct Funct Genomics (2010) 0.79
Using structure to explore the sequence alignment space of remote homologs. PLoS Comput Biol (2011) 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
VISTAL--a new 2D visualization tool of protein 3D structural alignments. Bioinformatics (2006) 0.77
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