PubRank

Ruben Abagyan

Author PubWeight™ 191.82‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 2006 15.00
2 Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 2010 10.30
3 METLIN: a metabolite mass spectral database. Ther Drug Monit 2005 10.15
4 Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science 2007 5.49
5 Structure of the human histamine H1 receptor complex with doxepin. Nature 2011 3.48
6 Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol 2010 3.38
7 Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des 2003 3.29
8 Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics 2005 2.83
9 Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc 2010 2.62
10 Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 2008 2.38
11 Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 2011 2.11
12 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
13 Nuclear hormone receptor targeted virtual screening. J Med Chem 2003 2.05
14 Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem 2010 1.88
15 Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004 1.79
16 The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol 2006 1.70
17 Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005 1.69
18 ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics 2006 1.68
19 Statistical analysis and prediction of protein-protein interfaces. Proteins 2005 1.65
20 ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003 1.63
21 Soft protein-protein docking in internal coordinates. Protein Sci 2002 1.60
22 GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins 2010 1.57
23 Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics 2002 1.56
24 Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci 2006 1.55
25 Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem 2009 1.54
26 Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci U S A 2003 1.53
27 Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science 2002 1.52
28 The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. Nat Rev Drug Discov 2012 1.50
29 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
30 Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform 2004 1.42
31 Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem 2008 1.38
32 Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des 2012 1.34
33 Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology 2010 1.31
34 Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 2006 1.29
35 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
36 A new method for publishing three-dimensional content. PLoS One 2009 1.23
37 PIER: protein interface recognition for structural proteomics. Proteins 2007 1.22
38 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
39 Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res 2011 1.21
40 Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates. J Med Chem 2007 1.21
41 Predictions of protein flexibility: first-order measures. Proteins 2004 1.21
42 Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal 2011 1.20
43 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
44 Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model 2010 1.17
45 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
46 Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol 2002 1.14
47 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
48 Structure-based discovery of natural-product-like TNF-α inhibitors. Angew Chem Int Ed Engl 2010 1.13
49 Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor. Mol Pharmacol 2009 1.12
50 Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J Chem Inf Model 2009 1.11
51 Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology 2010 1.10
52 FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics 2009 1.09
53 Defining the CD59-C9 binding interaction. J Biol Chem 2006 1.09
54 Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell 2013 1.07
55 A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des 2008 1.07
56 A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl 2012 1.06
57 Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. J Biol Chem 2011 1.06
58 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
59 Determinants of retinoid X receptor transcriptional antagonism. J Med Chem 2004 1.05
60 SGC--structural biology and human health: a new approach to publishing structural biology results. PLoS One 2009 1.02
61 Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure 2011 1.01
62 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
63 Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention. J Med Chem 2010 1.00
64 Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One 2011 0.99
65 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
66 ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. J Comput Chem 2003 0.99
67 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
68 Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 2005 0.97
69 Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One 2013 0.96
70 The transthyretin-related protein family. Eur J Biochem 2003 0.96
71 Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues. J Biol Chem 2007 0.96
72 Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity. Bioorg Med Chem Lett 2004 0.95
73 Ligand-guided receptor optimization. Methods Mol Biol 2012 0.94
74 ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. J Chem Inf Model 2012 0.94
75 Insights into the human CD59 complement binding interface toward engineering new therapeutics. J Biol Chem 2005 0.94
76 GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci 2011 0.93
77 Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Mol Pharmacol 2013 0.93
78 Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. J Med Chem 2012 0.93
79 Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des 2010 0.92
80 Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening. Biochem Biophys Res Commun 2007 0.92
81 Algorithms for high-density oligonucleotide array. Curr Opin Drug Discov Devel 2003 0.92
82 Molecular basis for binding and subtype selectivity of 1,4-benzodiazepine antagonist ligands of the cholecystokinin receptor. J Biol Chem 2012 0.92
83 Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases. Annu Rev Pharmacol Toxicol 2012 0.92
84 Unusual arginine formations in protein function and assembly: rings, strings, and stacks. J Phys Chem B 2012 0.91
85 Optimization of high throughput virtual screening by combining shape-matching and docking methods. J Chem Inf Model 2008 0.91
86 Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins. J Med Chem 2005 0.91
87 Molecular modeling and mutagenesis of gap junction channels. Prog Biophys Mol Biol 2007 0.90
88 In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ Sci Technol 2014 0.90
89 REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics 2005 0.90
90 Druggability of SCF ubiquitin ligase-protein interfaces. Methods Enzymol 2005 0.90
91 Role of lysine187 within the second extracellular loop of the type A cholecystokinin receptor in agonist-induced activation. Use of complementary charge-reversal mutagenesis to define a functionally important interdomain interaction. Biochemistry 2007 0.89
92 Damped-dynamics flexible fitting. Biophys J 2008 0.89
93 A natural product-like inhibitor of NEDD8-activating enzyme. Chem Commun (Camb) 2011 0.88
94 Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. J Biol Chem 2013 0.87
95 Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation. J Biol Chem 2009 0.87
96 The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening. J Med Chem 2010 0.87
97 Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem 2012 0.87
98 Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A. Anal Chem 2006 0.87
99 De novo discovery of serotonin N-acetyltransferase inhibitors. J Med Chem 2007 0.86
100 Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model 2014 0.86
101 Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophys J 2007 0.86
102 SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. Bioinformatics 2010 0.84
103 A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway. Cancer Res 2009 0.84
104 Identification of a new class of FtsZ inhibitors by structure-based design and in vitro screening. J Chem Inf Model 2013 0.84
105 Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling. Biochemistry 2009 0.84
106 Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations. J Mol Graph Model 2008 0.84
107 Methods of protein structure comparison. Methods Mol Biol 2012 0.84
108 Predicting p Ka values from EEM atomic charges. J Cheminform 2013 0.83
109 A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer. Methods Mol Biol 2013 0.82
110 Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. Eur J Med Chem 2011 0.82
111 Discovery of bioactive small-molecule inhibitor of poly adp-ribose polymerase: implications for energy-deficient cells. Chem Biol 2006 0.82
112 DFprot: a webtool for predicting local chain deformability. Bioinformatics 2007 0.82
113 Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J Comput Aided Mol Des 2007 0.82
114 New method for the assessment of all drug-like pockets across a structural genome. J Comput Biol 2008 0.82
115 The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers. Mol Pharmacol 2013 0.81
116 Discovery of novel membrane binding structures and functions. Biochem Cell Biol 2014 0.80
117 Interactive JIMD articles using the iSee concept: turning a new page on structural biology data. J Inherit Metab Dis 2011 0.80
118 Surrogate data--a secure way to share corporate data. J Comput Aided Mol Des 2005 0.80
119 Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Proteins 2008 0.80
120 Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. J Med Chem 2012 0.79
121 Weighted quality estimates in machine learning. Bioinformatics 2006 0.79
122 Screened charge electrostatic model in protein-protein docking simulations. Pac Symp Biocomput 2002 0.79
123 SAD--a normalized structural alignment database: improving sequence-structure alignments. Bioinformatics 2004 0.79
124 Self-assembling cannabinomimetics: supramolecular structures of N-alkyl amides. J Nat Prod 2007 0.78
125 Homology modeling of GPCRs. Methods Mol Biol 2009 0.78
126 Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization. J Med Chem 2012 0.78
127 Preparation and refinement of model protein-ligand complexes. Methods Mol Biol 2012 0.78
128 Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. Future Med Chem 2014 0.78
129 Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods Mol Biol 2015 0.77
130 Structure-based approaches to antibiotic drug discovery. Curr Protoc Microbiol 2009 0.77
131 Molecular modeling and in vitro reactivation study between the oxime BI-6 and acetylcholinesterase inhibited by different nerve agents. J Biomol Struct Dyn 2014 0.76
132 Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors. Eur J Med Chem 2012 0.76
133 Validation of the AmpC β-lactamase binding site and identification of inhibitors with novel scaffolds. J Chem Inf Model 2012 0.76
134 Structure-based design, synthesis, and biological evaluation of isatin derivatives as potential glycosyltransferase inhibitors. Chem Biol Drug Des 2014 0.76
135 Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theor Biol Med Model 2013 0.76
136 Sequence-conserved and antibody-accessible sites in the V1V2 domain of HIV-1 gp120 envelope protein. AIDS Res Hum Retroviruses 2014 0.76
137 Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors. Chem Biol Drug Des 2013 0.75
138 Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. J Comput Aided Mol Des 2011 0.75
139 Corrigendum: Lanosterol reverses protein aggregation in cataracts. Nature 2015 0.75
140 Computational evidence for the reactivation process of human acetylcholinesterase inhibited by carbamates. Comb Chem High Throughput Screen 2014 0.75
141 Correction to Environmental Photochemistry of Altrenogest: Photoisomerization to a Bioactive Product with Increased Environmental Persistence via Reversible Photohydration. Environ Sci Technol 2016 0.75