PubRank

Barry Honig

Author PubWeight™ 154.14‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 The role of DNA shape in protein-DNA recognition. Nature 2009 5.52
2 A hierarchical approach to all-atom protein loop prediction. Proteins 2004 5.18
3 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
4 Origins of specificity in protein-DNA recognition. Annu Rev Biochem 2010 4.43
5 GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol 2003 3.58
6 Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 2011 3.40
7 Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 2012 3.37
8 Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 2007 3.34
9 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
10 Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 2003 3.04
11 Type II cadherin ectodomain structures: implications for classical cadherin specificity. Cell 2006 2.85
12 On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol 2002 2.73
13 Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol 2006 2.37
14 Identification of a chloride ion binding site in Na+/Cl -dependent transporters. Proc Natl Acad Sci U S A 2007 2.32
15 The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure 2011 2.19
16 Electrostatic control of the membrane targeting of C2 domains. Mol Cell 2002 2.18
17 Protein structure prediction: inroads to biology. Mol Cell 2005 2.08
18 Outcome of a workshop on applications of protein models in biomedical research. Structure 2009 2.05
19 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
20 Cadherin-mediated cell-cell adhesion: sticking together as a family. Curr Opin Struct Biol 2003 1.94
21 On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins 2006 1.90
22 Loop modeling: Sampling, filtering, and scoring. Proteins 2008 1.81
23 On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 2006 1.79
24 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
25 Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature 2011 1.73
26 Thinking outside the cell: how cadherins drive adhesion. Trends Cell Biol 2012 1.72
27 Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle. Structure 2005 1.71
28 Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol 2010 1.70
29 Searching for neuronal left/right asymmetry: genomewide analysis of nematode receptor-type guanylyl cyclases. Genetics 2006 1.68
30 Splice form dependence of beta-neurexin/neuroligin binding interactions. Neuron 2010 1.68
31 Two-step adhesive binding by classical cadherins. Nat Struct Mol Biol 2010 1.67
32 On the role of electrostatic interactions in the design of protein-protein interfaces. J Mol Biol 2002 1.65
33 PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res 2012 1.59
34 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
35 Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res 2007 1.40
36 Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. J Mol Biol 2006 1.39
37 T-cadherin structures reveal a novel adhesive binding mechanism. Nat Struct Mol Biol 2010 1.37
38 A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol 2011 1.35
39 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
40 Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. J Mol Biol 2009 1.34
41 Nuance in the double-helix and its role in protein-DNA recognition. Curr Opin Struct Biol 2009 1.32
42 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
43 Helical packing patterns in membrane and soluble proteins. Biophys J 2004 1.30
44 An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans. Development 2006 1.26
45 Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins 2008 1.25
46 PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res 2011 1.25
47 Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity. J Mol Biol 2004 1.24
48 Comparative study of generalized born models: Born radii and peptide folding. J Phys Chem B 2005 1.24
49 Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. Structure 2008 1.24
50 Structural genomics: computational methods for structure analysis. Protein Sci 2003 1.24
51 Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol 2009 1.23
52 Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering. Proteins 2006 1.18
53 Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol 2011 1.14
54 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
55 Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J 2007 1.10
56 Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn 2010 1.08
57 Comparative study of generalized Born models: protein dynamics. Proc Natl Acad Sci U S A 2005 1.08
58 Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4. Structure 2008 1.07
59 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
60 An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins 2005 1.07
61 Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions. Mol Cell 2012 1.05
62 Nectin ectodomain structures reveal a canonical adhesive interface. Nat Struct Mol Biol 2012 1.04
63 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
64 Prediction of side-chain conformations on protein surfaces. Proteins 2007 1.03
65 Loop L5 acts as a conformational latch in the mitotic kinesin Eg5. J Biol Chem 2010 1.02
66 Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A 2007 1.01
67 Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains. J Mol Biol 2003 1.01
68 Local quality assessment in homology models using statistical potentials and support vector machines. Protein Sci 2007 1.00
69 Lozenge directly activates argos and klumpfuss to regulate programmed cell death. Genes Dev 2005 1.00
70 An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys J 2004 1.00
71 Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. J Biol Chem 2008 0.99
72 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
73 Theory and simulations of adhesion receptor dimerization on membrane surfaces. Biophys J 2013 0.97
74 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
75 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
76 Structural bioinformatics of the interactome. Annu Rev Biophys 2014 0.93
77 Protein structure space is much more than the sum of its folds. Nat Struct Mol Biol 2007 0.93
78 Using systems and structure biology tools to dissect cellular phenotypes. J Am Med Inform Assoc 2011 0.92
79 Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin. J Mol Biol 2011 0.91
80 Biophysics: Flipping Watson and Crick. Nature 2011 0.91
81 VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. PLoS Comput Biol 2010 0.90
82 MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Res 2011 0.89
83 Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold. Protein Sci 2003 0.88
84 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
85 Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Proc Natl Acad Sci U S A 2008 0.87
86 Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion. Proc Natl Acad Sci U S A 2013 0.86
87 OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res 2013 0.85
88 Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci 2003 0.84
89 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
90 Toward a "structural BLAST": using structural relationships to infer function. Protein Sci 2013 0.83
91 NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle. Proteins 2004 0.82
92 NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif. Proteins 2007 0.82
93 To B or not to B: PIP2 answers the question. Dev Cell 2005 0.81
94 Crystal structures of MTH1187 and its yeast ortholog YBL001c. Proteins 2003 0.81
95 Bending in the right direction. Structure 2005 0.80
96 Using structure to explore the sequence alignment space of remote homologs. PLoS Comput Biol 2011 0.79
97 High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J Struct Funct Genomics 2010 0.79
98 PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Res 2010 0.79
99 NMR structure of protein PA2021 from Pseudomonas aeruginosa. Proteins 2006 0.78
100 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
101 VISTAL--a new 2D visualization tool of protein 3D structural alignments. Bioinformatics 2006 0.77
102 Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. J Struct Funct Genomics 2012 0.76
103 Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. Proteins 2010 0.75
104 Bioinformatics in structural genomics. Bioinformatics 2002 0.75
105 Bridging worlds. Interview by Kristie Nybo. Biotechniques 2011 0.75
106 Mutli-features Predction of Protein Translational Modification Sites. IEEE/ACM Trans Comput Biol Bioinform 2017 0.75