Published in J Med Chem on December 25, 2008
Discovery of a novel mode of protein kinase inhibition characterized by the mechanism of inhibition of human mesenchymal-epithelial transition factor (c-Met) protein autophosphorylation by ARQ 197. J Biol Chem (2011) 1.45
Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des (2012) 1.34
Exploration of type II binding mode: A privileged approach for kinase inhibitor focused drug discovery? ACS Chem Biol (2014) 1.23
Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res (2011) 1.21
Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model (2010) 1.17
Rational approaches to improving selectivity in drug design. J Med Chem (2012) 1.16
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase. Proc Natl Acad Sci U S A (2013) 1.14
The flexible pocketome engine for structural chemogenomics. Methods Mol Biol (2009) 1.11
Discovery of Small Molecule RIP1 Kinase Inhibitors for the Treatment of Pathologies Associated with Necroptosis. ACS Med Chem Lett (2013) 1.04
p38α MAPK pathway: a key factor in colorectal cancer therapy and chemoresistance. World J Gastroenterol (2014) 1.02
Protein kinase-inhibitor database: structural variability of and inhibitor interactions with the protein kinase P-loop. J Proteome Res (2010) 0.92
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des (2010) 0.92
A novel mode of protein kinase inhibition exploiting hydrophobic motifs of autoinhibited kinases: discovery of ATP-independent inhibitors of fibroblast growth factor receptor. J Biol Chem (2011) 0.89
Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases. Curr Pharm Des (2012) 0.85
Virtual screening and optimization of Type II inhibitors of JAK2 from a natural product library. Chem Commun (Camb) (2014) 0.83
Lestaurtinib inhibits histone phosphorylation and androgen-dependent gene expression in prostate cancer cells. PLoS One (2012) 0.82
Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study. J Chem Theory Comput (2013) 0.82
Activity of the Ste20-like kinase, SLK, is enhanced by homodimerization. Am J Physiol Renal Physiol (2011) 0.81
Predicting inactive conformations of protein kinases using active structures: conformational selection of type-II inhibitors. PLoS One (2011) 0.81
Functional loop dynamics of the streptavidin-biotin complex. Sci Rep (2015) 0.80
Sorafenib inhibits p38α activity in colorectal cancer cells and synergizes with the DFG-in inhibitor SB202190 to increase apoptotic response. Cancer Biol Ther (2012) 0.80
Insights from free-energy calculations: protein conformational equilibrium, driving forces, and ligand-binding modes. Biophys J (2012) 0.80
Reversal of acquired drug resistance in FLT3-mutated acute myeloid leukemia cells via distinct drug combination strategies. Clin Cancer Res (2014) 0.79
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem (2014) 0.78
Novel VEGFR-2 kinase inhibitors identified by the back-to-front approach. Bioorg Med Chem Lett (2013) 0.78
DFGmodel: predicting protein kinase structures in inactive states for structure-based discovery of type-II inhibitors. ACS Chem Biol (2014) 0.78
c-Src binds to the cancer drug Ruxolitinib with an active conformation. PLoS One (2014) 0.77
Fragment-Based Discovery of a Dual pan-RET/VEGFR2 Kinase Inhibitor Optimized for Single-Agent Polypharmacology. Angew Chem Int Ed Engl (2015) 0.76
Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study. J Mol Graph Model (2015) 0.76
Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring. Proteins (2011) 0.76
Classifying kinase conformations using a machine learning approach. BMC Bioinformatics (2017) 0.75
PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun (2014) 0.75
Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design. J Comput Aided Mol Des (2016) 0.75
Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction. Mol Inform (2016) 0.75
Molecular modeling study of the induced-fit effect on kinase inhibition: the case of fibroblast growth factor receptor 3 (FGFR3). J Comput Aided Mol Des (2015) 0.75
Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors. J Comput Aided Mol Des (2011) 0.75
Characterization of interactions and pharmacophore development for DFG-out inhibitors to RET tyrosine kinase. J Mol Model (2015) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
The protein kinase complement of the human genome. Science (2002) 35.36
The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66
A quantitative analysis of kinase inhibitor selectivity. Nat Biotechnol (2008) 14.74
A small molecule-kinase interaction map for clinical kinase inhibitors. Nat Biotechnol (2005) 12.22
The Uppsala Electron-Density Server. Acta Crystallogr D Biol Crystallogr (2004) 9.60
Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science (2000) 9.29
Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. Cancer Cell (2005) 7.99
Protein kinases--the major drug targets of the twenty-first century? Nat Rev Drug Discov (2002) 7.38
Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol (2007) 6.56
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol (1994) 6.41
Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol (2006) 5.03
Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc Natl Acad Sci U S A (2006) 4.45
Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res (2002) 4.19
Features of selective kinase inhibitors. Chem Biol (2005) 4.07
Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Nat Struct Biol (2002) 3.92
A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc Natl Acad Sci U S A (2007) 3.21
Activation of tyrosine kinases by mutation of the gatekeeper threonine. Nat Struct Mol Biol (2008) 3.18
Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins (1997) 3.02
Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry (2007) 3.01
A general strategy for creating "inactive-conformation" abl inhibitors. Chem Biol (2006) 2.27
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol (2007) 2.13
On evaluating molecular-docking methods for pose prediction and enrichment factors. J Chem Inf Model (2006) 1.90
c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty. Structure (2007) 1.87
Structure of the carboxyl-terminal Src kinase, Csk. J Biol Chem (2002) 1.77
NS-187, a potent and selective dual Bcr-Abl/Lyn tyrosine kinase inhibitor, is a novel agent for imatinib-resistant leukemia. Blood (2005) 1.67
The RET kinase inhibitor NVP-AST487 blocks growth and calcitonin gene expression through distinct mechanisms in medullary thyroid cancer cells. Cancer Res (2007) 1.65
Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. Acta Crystallogr D Biol Crystallogr (2006) 1.61
Kinase inhibition with BAY 43-9006 in renal cell carcinoma. Clin Cancer Res (2004) 1.59
Protein variety and functional diversity: Swiss-Prot annotation in its biological context. C R Biol (2005) 1.54
Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit (2000) 1.46
Design and discovery of small molecules targeting raf-1 kinase. Curr Pharm Des (2002) 1.34
Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem Biol Drug Des (2007) 1.22
A new paradigm for protein kinase inhibition: blocking phosphorylation without directly targeting ATP binding. Drug Discov Today (2007) 1.19
Discovery of novel benzimidazoles as potent inhibitors of TIE-2 and VEGFR-2 tyrosine kinase receptors. J Med Chem (2007) 1.17
Discovery of N-(4-(3-amino-1H-indazol-4-yl)phenyl)-N'-(2-fluoro-5-methylphenyl)urea (ABT-869), a 3-aminoindazole-based orally active multitargeted receptor tyrosine kinase inhibitor. J Med Chem (2007) 1.11
Prevention of MKK6-dependent activation by binding to p38alpha MAP kinase. Biochemistry (2005) 1.11
Discovery of aryl aminoquinazoline pyridones as potent, selective, and orally efficacious inhibitors of receptor tyrosine kinase c-Kit. J Med Chem (2008) 1.08
Ligand binding affinity determined by temperature-dependent circular dichroism: cyclin-dependent kinase 2 inhibitors. Anal Biochem (2005) 1.06
Identification of ligand binding by protein stabilization: comparison of ATLAS with biophysical and enzymatic methods. Assay Drug Dev Technol (2008) 1.06
Kinetic studies of small molecule interactions with protein kinases using biosensor technology. Anal Biochem (2005) 1.01
Antileukemic effects of the novel, mutant FLT3 inhibitor NVP-AST487: effects on PKC412-sensitive and -resistant FLT3-expressing cells. Blood (2008) 1.01
Design, synthesis, and evaluation of orally active benzimidazoles and benzoxazoles as vascular endothelial growth factor-2 receptor tyrosine kinase inhibitors. J Med Chem (2007) 0.92
BIRB-796 is not an effective ABL(T315I) inhibitor. Nat Biotechnol (2005) 0.87
Structural factors contributing to the Abl/Lyn dual inhibitory activity of 3-substituted benzamide derivatives. Bioorg Med Chem Lett (2007) 0.85
Synthesis, structural analysis, and SAR studies of triazine derivatives as potent, selective Tie-2 inhibitors. Bioorg Med Chem Lett (2007) 0.83
Discovery of orally active pyrrolopyridine- and aminopyridine-based Met kinase inhibitors. Bioorg Med Chem Lett (2008) 0.81
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 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
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
Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc (2010) 2.62
Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38
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
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
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
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
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
Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42
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
A new method for publishing three-dimensional content. PLoS One (2009) 1.23
PIER: protein interface recognition for structural proteomics. Proteins (2007) 1.22
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
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
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
Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell (2013) 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
A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl (2012) 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
Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. J Biol Chem (2011) 1.06
Determinants of retinoid X receptor transcriptional antagonism. J Med Chem (2004) 1.05
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
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
Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One (2013) 0.96
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
The transthyretin-related protein family. Eur J Biochem (2003) 0.96
Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity. Bioorg Med Chem Lett (2004) 0.95
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. J Chem Inf Model (2012) 0.94
Ligand-guided receptor optimization. Methods Mol Biol (2012) 0.94
Insights into the human CD59 complement binding interface toward engineering new therapeutics. J Biol Chem (2005) 0.94
GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci (2011) 0.93
Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Mol Pharmacol (2013) 0.93
Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. J Med Chem (2012) 0.93
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
Algorithms for high-density oligonucleotide array. Curr Opin Drug Discov Devel (2003) 0.92
Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases. Annu Rev Pharmacol Toxicol (2012) 0.92
Molecular basis for binding and subtype selectivity of 1,4-benzodiazepine antagonist ligands of the cholecystokinin receptor. J Biol Chem (2012) 0.92
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des (2010) 0.92
Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins. J Med Chem (2005) 0.91
Unusual arginine formations in protein function and assembly: rings, strings, and stacks. J Phys Chem B (2012) 0.91
Optimization of high throughput virtual screening by combining shape-matching and docking methods. J Chem Inf Model (2008) 0.91
Molecular modeling and mutagenesis of gap junction channels. Prog Biophys Mol Biol (2007) 0.90
In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ Sci Technol (2014) 0.90
REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics (2005) 0.90
Druggability of SCF ubiquitin ligase-protein interfaces. Methods Enzymol (2005) 0.90
Damped-dynamics flexible fitting. Biophys J (2008) 0.89
A natural product-like inhibitor of NEDD8-activating enzyme. Chem Commun (Camb) (2011) 0.88
Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. J Biol Chem (2013) 0.87
The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening. J Med Chem (2010) 0.87
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
Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem (2012) 0.87
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
Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model (2014) 0.86
Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophys J (2007) 0.86
De novo discovery of serotonin N-acetyltransferase inhibitors. J Med Chem (2007) 0.86