Published in J Phys Chem B on April 19, 2012
HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis. Nature (2016) 1.39
Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors. Proc Natl Acad Sci U S A (2015) 1.01
Computational design of a self-assembling symmetrical β-propeller protein. Proc Natl Acad Sci U S A (2014) 0.98
The mitochondrial fission receptor MiD51 requires ADP as a cofactor. Structure (2014) 0.91
Crystal structure of Bax bound to the BH3 peptide of Bim identifies important contacts for interaction. Cell Death Dis (2015) 0.84
Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder. J Mol Biol (2015) 0.84
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. Nucleic Acids Res (2013) 0.80
Differential dimerization of variants linked to enhanced S-cone sensitivity syndrome (ESCS) located in the NR2E3 ligand-binding domain. Hum Mutat (2015) 0.79
3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7(T): crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Acta Crystallogr D Biol Crystallogr (2015) 0.77
Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability. Sci Rep (2017) 0.75
Anatomy of hot spots in protein interfaces. J Mol Biol (1998) 9.70
The Uppsala Electron-Density Server. Acta Crystallogr D Biol Crystallogr (2004) 9.60
The proteasome: paradigm of a self-compartmentalizing protease. Cell (1998) 8.43
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol (1988) 4.80
Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell (1999) 4.57
X-ray structures of the hexameric building block of the HIV capsid. Cell (2009) 4.08
Arginine-mediated RNA recognition: the arginine fork. Science (1991) 3.89
The structural biology of HIV assembly. Curr Opin Struct Biol (2008) 3.71
Amino-aromatic interactions in proteins. FEBS Lett (1986) 3.47
Ion-pairs in proteins. J Mol Biol (1983) 3.37
Protein structures forming the shell of primitive bacterial organelles. Science (2005) 3.20
Assembly properties of the human immunodeficiency virus type 1 CA protein. J Virol (2004) 3.09
Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci (1997) 3.00
Atomic-level modelling of the HIV capsid. Nature (2011) 2.41
Atomic-level models of the bacterial carboxysome shell. Science (2008) 2.36
An investigation of protein subunit and domain interfaces. Protein Eng (1988) 2.18
Planar stacking interactions of arginine and aromatic side-chains in proteins. J Mol Biol (1994) 1.97
The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core. Proc Natl Acad Sci U S A (2001) 1.94
Statistical analysis and prediction of protein-protein interfaces. Proteins (2005) 1.65
A twisted base? The role of arginine in enzyme-catalyzed proton abstractions. Arch Biochem Biophys (2005) 1.59
Structure and function of a mycobacterial NHEJ DNA repair polymerase. J Mol Biol (2006) 1.58
Structures of thymidine kinase 1 of human and mycoplasmic origin. Proc Natl Acad Sci U S A (2004) 1.56
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem (2009) 1.54
Molecular chaperones: containers and surfaces for folding, stabilising or unfolding proteins. Curr Opin Struct Biol (2000) 1.44
Contribution of unusual arginine-arginine short-range interactions to stabilization and recognition in proteins. J Protein Chem (1994) 1.41
Investigations on the maturation and regulation of archaebacterial proteasomes. J Mol Biol (2003) 1.32
Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J Biol Chem (2007) 1.27
Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J Biol Chem (2010) 1.26
The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans. Nat Struct Biol (2003) 1.26
PIER: protein interface recognition for structural proteomics. Proteins (2007) 1.22
In situ assembly of enzyme inhibitors using extended tethering. Nat Biotechnol (2003) 1.11
Structural basis of biopterin-induced inhibition of GTP cyclohydrolase I by GFRP, its feedback regulatory protein. J Biol Chem (2004) 1.11
Reversible ATP-dependent transition between two forms of human cytosolic thymidine kinase with different enzymatic properties. J Biol Chem (1993) 1.08
The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs). Protein Sci (2003) 1.05
An arginine ladder in OprP mediates phosphate-specific transfer across the outer membrane. Nat Struct Mol Biol (2006) 1.04
Computational mapping of anchoring spots on protein surfaces. J Mol Biol (2010) 1.02
Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative. J Biochem (2005) 0.99
The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family. Proteins (2007) 0.98
Crystal structure of a murine glutathione S-transferase in complex with a glutathione conjugate of 4-hydroxynon-2-enal in one subunit and glutathione in the other: evidence of signaling across the dimer interface. Biochemistry (1999) 0.96
Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J Mol Biol (2006) 0.90
Identification and characterization of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J Bacteriol (2006) 0.89
Evidence for an essential arginine recognition site on adenosine 3':5'-cyclic monophosphate-dependent protein kinase of rabbit skeletal muscle. Biochem J (1978) 0.89
The first structure of a cold-active catalase from Vibrio salmonicida at 1.96 A reveals structural aspects of cold adaptation. Acta Crystallogr D Biol Crystallogr (2007) 0.86
The dodecin from Thermus thermophilus, a bifunctional cofactor storage protein. J Biol Chem (2007) 0.84
Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales. J Mol Biol (2007) 0.83
Analysis of Streptomyces coelicolor phosphopantetheinyl transferase, AcpS, reveals the basis for relaxed substrate specificity. Biochemistry (2011) 0.81
Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans. J Mol Biol (2004) 0.80
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem (2006) 15.00
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (2010) 10.30
METLIN: a metabolite mass spectral database. Ther Drug Monit (2005) 10.15
Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science (2007) 5.49
Structure of full-length HIV-1 CA: a model for the mature capsid lattice. Cell (2007) 4.25
X-ray structures of the hexameric building block of the HIV capsid. Cell (2009) 4.08
The structural biology of HIV assembly. Curr Opin Struct Biol (2008) 3.71
Structure of the human histamine H1 receptor complex with doxepin. Nature (2011) 3.48
Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol (2010) 3.38
Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell (2006) 3.36
Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29
Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics (2005) 2.83
Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Mol Cell (2003) 2.78
Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc (2010) 2.62
Atomic-level modelling of the HIV capsid. Nature (2011) 2.41
Hexagonal assembly of a restricting TRIM5alpha protein. Proc Natl Acad Sci U S A (2010) 2.40
Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38
Reduction of ischemia and reperfusion-induced myocardial damage by cytochrome P450 inhibitors. Proc Natl Acad Sci U S A (2004) 2.11
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (2011) 2.11
Nuclear hormone receptor targeted virtual screening. J Med Chem (2003) 2.05
Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J Mol Recognit (2009) 2.05
Three-dimensional EM structure of the ectodomain of integrin {alpha}V{beta}3 in a complex with fibronectin. J Cell Biol (2005) 1.97
Solution state characterization of amyloid beta-derived diffusible ligands. Biochemistry (2006) 1.96
Three-dimensional model of the human platelet integrin alpha IIbbeta 3 based on electron cryomicroscopy and x-ray crystallography. Proc Natl Acad Sci U S A (2002) 1.93
Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem (2010) 1.88
Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol (2004) 1.79
The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol (2006) 1.70
Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins (2005) 1.69
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics (2006) 1.68
Statistical analysis and prediction of protein-protein interfaces. Proteins (2005) 1.65
Ultrastructural and biophysical characterization of hepatitis C virus particles produced in cell culture. J Virol (2010) 1.64
ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins (2003) 1.63
Soft protein-protein docking in internal coordinates. Protein Sci (2002) 1.60
Three-dimensional structure of the M-MuLV CA protein on a lipid monolayer: a general model for retroviral capsid assembly. EMBO J (2003) 1.58
GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins (2010) 1.57
Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics (2002) 1.56
Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci (2006) 1.55
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem (2009) 1.54
A Calpha model for the transmembrane alpha helices of gap junction intercellular channels. Mol Cell (2004) 1.54
Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci U S A (2003) 1.53
Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science (2002) 1.52
The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. Nat Rev Drug Discov (2012) 1.50
Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. J Comput Aided Mol Des (2009) 1.48
Native hepatitis B virions and capsids visualized by electron cryomicroscopy. Mol Cell (2006) 1.44
Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42
Complementarity in the supramolecular design of arenaviruses and retroviruses revealed by electron cryomicroscopy and image analysis. J Virol (2005) 1.40
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem (2008) 1.38
Nodavirus coat protein imposes dodecahedral RNA structure independent of nucleotide sequence and length. J Virol (2004) 1.35
Disulfide bond stabilization of the hexameric capsomer of human immunodeficiency virus. J Mol Biol (2010) 1.35
Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy. J Virol (2006) 1.34
Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des (2012) 1.34
Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology (2010) 1.31
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins (2006) 1.29
Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands. J Med Chem (2009) 1.28
Assembly and architecture of HIV. Adv Exp Med Biol (2012) 1.26
An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. Proc Natl Acad Sci U S A (2005) 1.24
A new method for publishing three-dimensional content. PLoS One (2009) 1.23
Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling. J Biol Chem (2011) 1.22
PIER: protein interface recognition for structural proteomics. Proteins (2007) 1.22
Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res (2011) 1.21
Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates. J Med Chem (2007) 1.21
Predictions of protein flexibility: first-order measures. Proteins (2004) 1.21
Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal (2011) 1.20
3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A (2007) 1.20
Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model (2010) 1.17
Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol Pharmacol (2007) 1.16
Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol (2002) 1.14
Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping. FASEB J (2012) 1.13
Structure-based discovery of natural-product-like TNF-α inhibitors. Angew Chem Int Ed Engl (2010) 1.13
Effects of blocking individual maturation cleavages in murine leukemia virus gag. J Virol (2004) 1.12
Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor. Mol Pharmacol (2009) 1.12
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J Chem Inf Model (2009) 1.11
Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology (2010) 1.10
FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics (2009) 1.09
Defining the CD59-C9 binding interaction. J Biol Chem (2006) 1.09
Virus-like particles of a fish nodavirus display a capsid subunit domain organization different from that of insect nodaviruses. J Virol (2002) 1.09
Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell (2013) 1.07
Dynamics and stability in maturation of a T=4 virus. J Mol Biol (2009) 1.07
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des (2008) 1.07
Single-particle image reconstruction of a tetramer of HIV integrase bound to DNA. J Mol Biol (2006) 1.07
A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl (2012) 1.06
Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. J Biol Chem (2011) 1.06
Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding. Mol Pharmacol (2008) 1.06
Determinants of retinoid X receptor transcriptional antagonism. J Med Chem (2004) 1.05
Imaging flow cytometry elucidates limitations of microparticle analysis by conventional flow cytometry. Cytometry A (2014) 1.04
Identification and characterization of Vnx1p, a novel type of vacuolar monovalent cation/H+ antiporter of Saccharomyces cerevisiae. J Biol Chem (2007) 1.03
A viral nanoparticle with dual function as an anthrax antitoxin and vaccine. PLoS Pathog (2007) 1.02
SGC--structural biology and human health: a new approach to publishing structural biology results. PLoS One (2009) 1.02
Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure (2011) 1.01
Profiling of membrane protein variants in a baculovirus system by coupling cell-surface detection with small-scale parallel expression. Protein Expr Purif (2007) 1.01
Secretin occupies a single protomer of the homodimeric secretin receptor complex: insights from photoaffinity labeling studies using dual sites of covalent attachment. J Biol Chem (2010) 1.01
Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention. J Med Chem (2010) 1.00
Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One (2011) 0.99
Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes. J Chem Inf Model (2011) 0.99
ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. J Comput Chem (2003) 0.99
Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J Biol Chem (2007) 0.98
Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins (2005) 0.97