Published in J Comput Aided Mol Des on March 27, 2007
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des (2013) 2.93
Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol (2009) 2.84
Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput Biol (2009) 2.35
Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput Biol (2011) 2.31
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nat Chem (2013) 2.26
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol (2007) 2.13
Recommendations for evaluation of computational methods. J Comput Aided Mol Des (2008) 1.87
Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74
Variability in docking success rates due to dataset preparation. J Comput Aided Mol Des (2012) 1.54
How to do an evaluation: pitfalls and traps. J Comput Aided Mol Des (2008) 1.43
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol (2007) 1.40
Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des (2012) 1.27
Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5). J Biol Chem (2011) 1.25
Bias, reporting, and sharing: computational evaluations of docking methods. J Comput Aided Mol Des (2007) 1.21
CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model (2013) 1.17
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des (2009) 1.11
Customizing scoring functions for docking. J Comput Aided Mol Des (2008) 1.11
A novel small molecule antagonist of choline kinase-α that simultaneously suppresses MAPK and PI3K/AKT signaling. Oncogene (2011) 1.09
FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J Chem Inf Model (2012) 1.09
Structural studies of pterin-based inhibitors of dihydropteroate synthase. J Med Chem (2010) 1.04
The eccentric cleavage product of β-carotene, β-apo-13-carotenone, functions as an antagonist of RXRα. Arch Biochem Biophys (2010) 1.04
Structure-based discovery of antibacterial drugs. Nat Rev Microbiol (2010) 1.04
Poly(ADP-ribose) catabolism triggers AMP-dependent mitochondrial energy failure. J Biol Chem (2009) 1.03
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J Comput Aided Mol Des (2007) 1.00
How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur Biophys J (2010) 0.99
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening. BMC Bioinformatics (2008) 0.99
Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex. J Chem Inf Model (2008) 0.98
Protein flexibility in docking and surface mapping. Q Rev Biophys (2012) 0.96
Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function. J Chem Inf Model (2011) 0.96
Experimental validation of FINDSITE(comb) virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. J Cheminform (2014) 0.94
Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization. Biochemistry (2009) 0.94
Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study. J Chem Inf Model (2014) 0.93
Mutagenesis and computer modeling studies of a GPCR conserved residue W5.43(194) in ligand recognition and signal transduction for CB2 receptor. Int Immunopharmacol (2011) 0.93
Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Curr Opin Struct Biol (2013) 0.93
Marine sponge-derived sipholane triterpenoids reverse P-glycoprotein (ABCB1)-mediated multidrug resistance in cancer cells. Biochem Pharmacol (2010) 0.92
Identification of novel non-hydroxamate anthrax toxin lethal factor inhibitors by topomeric searching, docking and scoring, and in vitro screening. J Chem Inf Model (2009) 0.92
Design, synthesis, docking, and biological evaluation of novel diazide-containing isoxazole- and pyrazole-based histone deacetylase probes. J Med Chem (2011) 0.90
Does your model weigh the same as a duck? J Comput Aided Mol Des (2011) 0.89
Conformationally constrained opioid ligands: the Dmt-Aba and Dmt-Aia versus Dmt-Tic scaffold. Bioorg Med Chem Lett (2008) 0.89
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction. BMC Bioinformatics (2010) 0.89
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics (2012) 0.88
Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments. Open Biochem J (2008) 0.86
Development of a comprehensive, validated pharmacophore hypothesis for anthrax toxin lethal factor (LF) inhibitors using genetic algorithms, Pareto scoring, and structural biology. J Chem Inf Model (2012) 0.86
A ligand's-eye view of protein binding. J Comput Aided Mol Des (2008) 0.86
Prediction and identification of T cell epitopes in the H5N1 influenza virus nucleoprotein in chicken. PLoS One (2012) 0.86
Carborane clusters in computational drug design: a comparative docking evaluation using AutoDock, FlexX, Glide, and Surflex. J Chem Inf Model (2009) 0.85
Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. J Comput Aided Mol Des (2015) 0.85
Drug design for ever, from hype to hope. J Comput Aided Mol Des (2012) 0.85
Application of consensus scoring and principal component analysis for virtual screening against β-secretase (BACE-1). PLoS One (2012) 0.84
Software and resources for computational medicinal chemistry. Future Med Chem (2011) 0.84
Intracellular β-nicotinamide adenine dinucleotide inhibits the skeletal muscle ClC-1 chloride channel. J Biol Chem (2012) 0.84
In silico prediction of estrogen receptor subtype binding affinity and selectivity using statistical methods and molecular docking with 2-arylnaphthalenes and 2-arylquinolines. Int J Mol Sci (2010) 0.84
Molecular docking and 3D-QSAR study on 4-(1H-indazol-4-yl) phenylamino and aminopyrazolopyridine urea derivatives as kinase insert domain receptor (KDR) inhibitors. J Mol Model (2011) 0.83
Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach. PLoS One (2014) 0.83
Novel insights of structure-based modeling for RNA-targeted drug discovery. J Chem Inf Model (2012) 0.82
Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily. Proc Natl Acad Sci U S A (2015) 0.82
Tyrosine kinase syk non-enzymatic inhibitors and potential anti-allergic drug-like compounds discovered by virtual and in vitro screening. PLoS One (2011) 0.82
Structure-based discovery of highly selective phosphodiesterase-9A inhibitors and implications for inhibitor design. J Med Chem (2012) 0.82
Probing the steric requirements of the γ-aminobutyric acid aminotransferase active site with fluorinated analogues of vigabatrin. Bioorg Med Chem (2012) 0.82
Discovery of N-{4-[(3-hydroxyphenyl)-3-methylpiperazin-1-yl]methyl-2-methylpropyl}-4-phenoxybenzamide analogues as selective kappa opioid receptor antagonists. J Med Chem (2013) 0.81
Structure-dependent binding of arylimidamides to the DNA minor groove. Chembiochem (2013) 0.81
Pkb/Akt1 mediates Wnt/GSK3β/β-catenin signaling-induced apoptosis in human cord blood stem cells exposed to organophosphate pesticide monocrotophos. Stem Cells Dev (2012) 0.81
Statistical analysis, optimization, and prioritization of virtual screening parameters for zinc enzymes including the anthrax toxin lethal factor. Curr Top Med Chem (2014) 0.80
Crystal structure of histamine dehydrogenase from Nocardioides simplex. J Biol Chem (2010) 0.79
Total synthesis and evaluation of C26-hydroxyepothilone D derivatives for photoaffinity labeling of beta-tubulin. J Org Chem (2010) 0.79
Virtual Screening Approaches towards the Discovery of Toll-Like Receptor Modulators. Int J Mol Sci (2016) 0.79
Structure-based Design Targeted at LOX-1, a Receptor for Oxidized Low-Density Lipoprotein. Sci Rep (2015) 0.78
Mechanistic insight into inhibition of two-component system signaling. Medchemcomm (2012) 0.78
Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins. BMC Bioinformatics (2015) 0.78
A structure-guided approach for protein pocket modeling and affinity prediction. J Comput Aided Mol Des (2013) 0.78
Pyrrolo[3,2-d]pyrimidine derivatives as type II kinase insert domain receptor (KDR) inhibitors: CoMFA and CoMSIA studies. Int J Mol Sci (2012) 0.78
Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification. J Chem Inf Model (2014) 0.78
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics (2016) 0.78
Insights from comprehensive multiple receptor docking to HDAC8. J Mol Model (2012) 0.78
Molecular docking and enzymatic evaluation to identify selective inhibitors of aspartate semialdehyde dehydrogenase. Bioorg Med Chem (2012) 0.78
Amiloride Analogs as ASIC1a Inhibitors. CNS Neurosci Ther (2016) 0.78
Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation. Sci Rep (2015) 0.77
The molecular basis for the inhibition of human cytochrome P450 1A2 by oroxylin and wogonin. Eur Biophys J (2012) 0.77
In silico identification of structure requirement for novel thiazole and oxazole derivatives as potent fructose 1,6-bisphosphatase inhibitors. Int J Mol Sci (2011) 0.77
Building a virtual ligand screening pipeline using free software: a survey. Brief Bioinform (2015) 0.77
Aminopyridyl/Pyrazinyl Spiro[indoline-3,4'-piperidine]-2-ones As Highly Selective and Efficacious c-Met/ALK Inhibitors. ACS Med Chem Lett (2013) 0.77
Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target. PLoS One (2013) 0.77
Mammary carcinogen-protein binding potentials: novel and biologically relevant structure-activity relationship model descriptors. SAR QSAR Environ Res (2010) 0.77
Insight into the interactions between novel isoquinolin-1,3-dione derivatives and cyclin-dependent kinase 4 combining QSAR and molecular docking. PLoS One (2014) 0.77
Structural and functional analyses of a sterol carrier protein in Spodoptera litura. PLoS One (2014) 0.77
Cloud computing approaches for prediction of ligand binding poses and pathways. Sci Rep (2015) 0.77
A strategy to discover decoy chemokine ligands with an anti-inflammatory activity. Sci Rep (2015) 0.76
Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform. Nucleic Acids Res (2009) 0.76
Selectivity of Imidacloprid for fruit fly versus rat nicotinic acetylcholine receptors by molecular modeling. J Mol Model (2009) 0.76
In-silico identification of the binding mode of synthesized adamantyl derivatives inside cholinesterase enzymes. Acta Pharmacol Sin (2015) 0.76
PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation. J Chem Inf Model (2016) 0.76
Synthesis and in silico screening of a library of β-carboline-containing compounds. Beilstein J Org Chem (2012) 0.76
Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations. J Mol Model (2013) 0.76
Global structure-activity relationship model for nonmutagenic carcinogens using virtual ligand-protein interactions as model descriptors. Carcinogenesis (2012) 0.76
Design, synthesis, crystallization and biological evaluation of new symmetrical biscationic compounds as selective inhibitors of human Choline Kinase α1 (ChoKα1). Sci Rep (2016) 0.76
Identification of novel anthrax toxin countermeasures using in silico methods. Methods Mol Biol (2013) 0.75
Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape. J Comput Chem (2015) 0.75
Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction. PLoS One (2013) 0.75
Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz (2015) 0.75
Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE). BMC Struct Biol (2012) 0.75
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem (2004) 15.51
Development and validation of a genetic algorithm for flexible docking. J Mol Biol (1997) 14.36
Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem (2006) 8.75
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem (2004) 7.96
Improved protein-ligand docking using GOLD. Proteins (2003) 7.94
A fast flexible docking method using an incremental construction algorithm. J Mol Biol (1996) 7.33
Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit (1996) 6.51
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem (2004) 6.50
A critical assessment of docking programs and scoring functions. J Med Chem (2006) 5.78
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des (1997) 5.71
Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des (2002) 5.65
Benchmarking sets for molecular docking. J Med Chem (2006) 5.57
Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem (2003) 4.49
Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des (1996) 3.78
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des (1994) 3.12
Comparison of shape-matching and docking as virtual screening tools. J Med Chem (2007) 3.09
Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem (2007) 3.03
A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem (1999) 2.98
Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol (2000) 2.86
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem (2000) 2.35
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins (2004) 2.17
Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins (2004) 2.12
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem (2002) 2.10
Deciphering common failures in molecular docking of ligand-protein complexes. J Comput Aided Mol Des (2000) 1.87
Parameter estimation for scoring protein-ligand interactions using negative training data. J Med Chem (2006) 1.71
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J Comput Aided Mol Des (2002) 1.68
Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol (1996) 1.61
Ligand-based structural hypotheses for virtual screening. J Med Chem (2004) 1.58
Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition. J Comput Aided Mol Des (2000) 1.35
Comparison of automated docking programs as virtual screening tools. J Med Chem (2005) 1.33
Scoring functions for protein-ligand docking. Curr Protein Pept Sci (2006) 1.29
Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. J Med Chem (1994) 1.27
Virtual screening in lead discovery and optimization. Curr Opin Drug Discov Devel (2004) 1.26
Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex. J Med Chem (2005) 1.22
Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. J Mol Model (2003) 1.20
Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins. J Med Chem (1999) 1.14
A shape-based machine learning tool for drug design. J Comput Aided Mol Des (1994) 1.13
Novel inhibitors of poly(ADP-ribose) polymerase/PARP1 and PARP2 identified using a cell-based screen in yeast. Cancer Res (2001) 1.09
Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. J Med Chem (1995) 1.01