Published in J Chem Inf Model on April 26, 2010
ZINC: a free tool to discover chemistry for biology. J Chem Inf Model (2012) 6.57
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem (2012) 2.86
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nat Chem (2013) 2.26
Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol (2014) 1.66
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. J Chem Inf Model (2011) 1.61
Blind prediction of solvation free energies from the SAMPL4 challenge. J Comput Aided Mol Des (2014) 1.40
FRED and HYBRID docking performance on standardized datasets. J Comput Aided Mol Des (2012) 1.36
PubChem3D: a new resource for scientists. J Cheminform (2011) 1.31
Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5). J Biol Chem (2011) 1.25
Confab - Systematic generation of diverse low-energy conformers. J Cheminform (2011) 1.18
CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model (2013) 1.17
Structural mechanism underlying capsaicin binding and activation of the TRPV1 ion channel. Nat Chem Biol (2015) 1.11
Probing the S1 specificity pocket of the aminopeptidases that generate antigenic peptides. Biochem J (2011) 1.10
Small-molecule 3D structure prediction using open crystallography data. J Chem Inf Model (2013) 1.10
ZINC 15 - Ligand Discovery for Everyone. J Chem Inf Model (2015) 1.07
Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds. J Am Chem Soc (2013) 1.05
Blind prediction of HIV integrase binding from the SAMPL4 challenge. J Comput Aided Mol Des (2014) 0.99
PubChem3D: Conformer generation. J Cheminform (2011) 0.99
Discovery of novel small-molecule inhibitors of BRD4 using structure-based virtual screening. J Med Chem (2013) 0.99
Ligand pose and orientational sampling in molecular docking. PLoS One (2013) 0.99
Predicting drug-target interactions using probabilistic matrix factorization. J Chem Inf Model (2013) 0.98
Generation of crystal structures using known crystal structures as analogues. Acta Crystallogr B Struct Sci Cryst Eng Mater (2016) 0.96
PubChem3D: conformer ensemble accuracy. J Cheminform (2013) 0.96
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis. J Cheminform (2012) 0.95
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure (2016) 0.93
Expanding the olfactory code by in silico decoding of odor-receptor chemical space. Elife (2013) 0.93
Diuresis and reduced urinary osmolality in rats produced by small-molecule UT-A-selective urea transport inhibitors. FASEB J (2014) 0.93
An integrated suite of modeling tools that empower scientists in structure- and property-based drug design. J Comput Aided Mol Des (2015) 0.93
LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. Bioinformatics (2014) 0.91
Understanding TRPV1 activation by ligands: Insights from the binding modes of capsaicin and resiniferatoxin. Proc Natl Acad Sci U S A (2015) 0.89
Docking challenge: protein sampling and molecular docking performance. J Chem Inf Model (2013) 0.89
Plant membrane assays with cytokinin receptors underpin the unique role of free cytokinin bases as biologically active ligands. J Exp Bot (2015) 0.88
Engineering an allosteric transcription factor to respond to new ligands. Nat Methods (2015) 0.87
Insights into the Modulation of Dopamine Transporter Function by Amphetamine, Orphenadrine, and Cocaine Binding. Front Neurol (2015) 0.86
Computation-guided discovery of influenza endonuclease inhibitors. ACS Med Chem Lett (2014) 0.86
Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface (2011) 0.86
Discovery of new liver X receptor agonists by pharmacophore modeling and shape-based virtual screening. J Chem Inf Model (2014) 0.85
Non-peptidic cruzain inhibitors with trypanocidal activity discovered by virtual screening and in vitro assay. PLoS Negl Trop Dis (2013) 0.85
Molecular docking screening using agonist-bound GPCR structures: probing the A2A adenosine receptor. J Chem Inf Model (2015) 0.83
Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling. J Comput Aided Mol Des (2014) 0.83
Ligand placement based on prior structures: the guided ligand-replacement method. Acta Crystallogr D Biol Crystallogr (2013) 0.83
Structural properties of non-traditional drug targets present new challenges for virtual screening. J Chem Inf Model (2013) 0.83
The identification of novel Mycobacterium tuberculosis DHFR inhibitors and the investigation of their binding preferences by using molecular modelling. Sci Rep (2015) 0.83
Novel mycosin protease MycP₁ inhibitors identified by virtual screening and 4D fingerprints. J Chem Inf Model (2014) 0.83
Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. J Comput Aided Mol Des (2014) 0.83
Ligand-based pharmacophore modeling and virtual screening for the discovery of novel 17β-hydroxysteroid dehydrogenase 2 inhibitors. J Med Chem (2014) 0.83
DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites. J Med Chem (2015) 0.82
Selectivity and evolutionary divergence of metabotropic glutamate receptors for endogenous ligands and G proteins coupled to phospholipase C or TRP channels. J Biol Chem (2014) 0.82
Shaping suvorexant: application of experimental and theoretical methods for driving synthetic designs. J Comput Aided Mol Des (2014) 0.82
LigandBox: A database for 3D structures of chemical compounds. Biophysics (Nagoya-shi) (2013) 0.82
Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water. J Chem Theory Comput (2016) 0.82
Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK. J Comput Aided Mol Des (2014) 0.82
Identification and Characterization of New Chemical Entities Targeting Apurinic/Apyrimidinic Endonuclease 1 for the Prevention of Chemotherapy-Induced Peripheral Neuropathy. J Pharmacol Exp Ther (2016) 0.82
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. PLoS Comput Biol (2015) 0.82
Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions. PLoS One (2015) 0.82
SMMRNA: a database of small molecule modulators of RNA. Nucleic Acids Res (2013) 0.82
Diamidine compounds for selective inhibition of protein arginine methyltransferase 1. J Med Chem (2014) 0.82
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des (2016) 0.82
PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions. Int J Mol Sci (2014) 0.81
How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? J Chem Inf Model (2015) 0.81
Inhibition of myeloperoxidase: evaluation of 2H-indazoles and 1H-indazolones. Bioorg Med Chem (2014) 0.81
Structure-activity relationship studies of indole-based compounds as small molecule HIV-1 fusion inhibitors targeting glycoprotein 41. J Med Chem (2014) 0.81
Identification of an Atg8-Atg3 protein-protein interaction inhibitor from the medicines for Malaria Venture Malaria Box active in blood and liver stage Plasmodium falciparum parasites. J Med Chem (2014) 0.81
Synthesis and assessment of catechol diether compounds as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1). Bioorg Med Chem Lett (2013) 0.81
Different effects of progesterone and estradiol on chimeric and wild type aldosterone synthase in vitro. Reprod Biol Endocrinol (2013) 0.81
Insights into the mechanism of inhibition of CXCR4: identification of Piperidinylethanamine analogs as anti-HIV-1 inhibitors. Antimicrob Agents Chemother (2015) 0.81
Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology. Br J Pharmacol (2013) 0.81
Bioactive conformational generation of small molecules: a comparative analysis between force-field and multiple empirical criteria based methods. BMC Bioinformatics (2010) 0.80
Computer-guided approach to access the anti-influenza activity of licorice constituents. J Nat Prod (2013) 0.80
PharmDock: a pharmacophore-based docking program. J Cheminform (2014) 0.80
Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction. J Comput Aided Mol Des (2011) 0.80
Virtual screening models for prediction of HIV-1 RT associated RNase H inhibition. PLoS One (2013) 0.80
Binding pocket optimization by computational protein design. PLoS One (2012) 0.80
A conserved amphipathic ligand binding region influences k-path-dependent activity of cytochrome C oxidase. Biochemistry (2013) 0.80
Protein pocket and ligand shape comparison and its application in virtual screening. J Comput Aided Mol Des (2013) 0.79
Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment. J Chem Inf Model (2015) 0.79
Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model (2014) 0.79
Shape-based virtual screening with volumetric aligned molecular shapes. J Comput Chem (2014) 0.79
Development and validation of an improved algorithm for overlaying flexible molecules. J Comput Aided Mol Des (2012) 0.79
Virtual Screening Approaches towards the Discovery of Toll-Like Receptor Modulators. Int J Mol Sci (2016) 0.79
Identification of FDA-approved drugs that computationally bind to MDM2. Chem Biol Drug Des (2012) 0.79
Using MD Simulations To Calculate How Solvents Modulate Solubility. J Chem Theory Comput (2016) 0.79
Fast docking on graphics processing units via Ray-Casting. PLoS One (2013) 0.79
Crystal Structure of an LSD-Bound Human Serotonin Receptor. Cell (2017) 0.79
The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A. Chem Commun (Camb) (2017) 0.79
BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J Cheminform (2015) 0.78
DFGmodel: predicting protein kinase structures in inactive states for structure-based discovery of type-II inhibitors. ACS Chem Biol (2014) 0.78
A systems chemical biology study of malate synthase and isocitrate lyase inhibition in Mycobacterium tuberculosis during active and NRP growth. Comput Biol Chem (2013) 0.78
Amiloride Analogs as ASIC1a Inhibitors. CNS Neurosci Ther (2016) 0.78
Targeting Lysine Deacetylases (KDACs) in Parasites. PLoS Negl Trop Dis (2015) 0.78
DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites. PLoS One (2015) 0.78
Base modification strategies to modulate immune stimulation by an siRNA. Chembiochem (2014) 0.78
Synthesis and Pharmacological Evolution of Tetrahydroisoquinolines as Anti Breast Cancer Agents. J Cancer Sci Ther (2014) 0.78
Evaluation of the Inhibitory Effects of Bavachinin and Bavachin on Human Monoamine Oxidases A and B. Evid Based Complement Alternat Med (2015) 0.78
Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN. J Mol Model (2015) 0.78
Inhibition of Sodium Ion Channel Function with Truncated Forms of Batrachotoxin. ACS Chem Neurosci (2016) 0.78
Virtual Screening of Peptide and Peptidomimetic Fragments Targeted to Inhibit Bacterial Dithiol Oxidase DsbA. PLoS One (2015) 0.77
Novel Activities of Select NSAID R-Enantiomers against Rac1 and Cdc42 GTPases. PLoS One (2015) 0.77
Inhibitor ranking through QM based chelation calculations for virtual screening of HIV-1 RNase H inhibition. PLoS One (2014) 0.77
ClogP(alk): a method for predicting alkane/water partition coefficient. J Comput Aided Mol Des (2013) 0.77
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr (1997) 137.43
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A (1991) 119.63
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (1992) 36.50
A critical assessment of docking programs and scoring functions. J Med Chem (2006) 5.78
The PDBbind database: methodologies and updates. J Med Chem (2005) 5.53
Remarks about protein structure precision. Acta Crystallogr D Biol Crystallogr (1999) 5.22
Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem (2007) 3.03
Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model (2003) 2.78
Validation of protein crystal structures. Acta Crystallogr D Biol Crystallogr (2000) 2.38
Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis. J Chem Inf Model (2008) 2.04
Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem (2004) 2.04
ASEDock-docking based on alpha spheres and excluded volumes. J Chem Inf Model (2008) 1.81
Generating conformer ensembles using a multiobjective genetic algorithm. J Chem Inf Model (2007) 1.80
Comparing protein-ligand docking programs is difficult. Proteins (2005) 1.60
Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J Mol Biol (1997) 1.50
Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations. J Chem Inf Model (2006) 1.44
Lingos, finite state machines, and fast similarity searching. J Chem Inf Model (2006) 1.44
How to do an evaluation: pitfalls and traps. J Comput Aided Mol Des (2008) 1.43
Frog: a FRee Online druG 3D conformation generator. Nucleic Acids Res (2007) 1.29
Rearrangement of Cruickshank's formulae for the diffraction-component precision index. Acta Crystallogr D Biol Crystallogr (2002) 1.27
CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration. J Chem Inf Model (2007) 1.18
Ph4Dock: pharmacophore-based protein-ligand docking. J Med Chem (2004) 1.14
Torsion angle preference and energetics of small-molecule ligands bound to proteins. J Chem Inf Model (2007) 1.13
Conformational sampling of druglike molecules with MOE and catalyst: implications for pharmacophore modeling and virtual screening. J Chem Inf Model (2008) 1.08
Conformational analysis by intersection: CONAN. J Comput Chem (2003) 1.04
Conformational sampling of bioactive molecules: a comparative study. J Chem Inf Model (2007) 1.04
Flexibases: a way to enhance the use of molecular docking methods. J Comput Aided Mol Des (1994) 1.00
An alternative method for the evaluation of docking performance: RSR vs RMSD. J Chem Inf Model (2008) 0.97
Comparison of conformational analysis techniques to generate pharmacophore hypotheses using catalyst. J Chem Inf Model (2005) 0.97
MIMUMBA revisited: torsion angle rules for conformer generation derived from X-ray structures. J Chem Inf Model (2006) 0.93
Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations. J Chem Inf Comput Sci (2001) 0.93
Distributed torsion angle grid search in high dimensions: a systematic approach to NMR structure determination. J Biomol NMR (1998) 0.88
Comparison of shape-matching and docking as virtual screening tools. J Med Chem (2007) 3.09
Conformer generation with OMEGA: learning from the data set and the analysis of failures. J Chem Inf Model (2012) 1.86
The SAMPL2 blind prediction challenge: introduction and overview. J Comput Aided Mol Des (2010) 1.53
How to do an evaluation: pitfalls and traps. J Comput Aided Mol Des (2008) 1.43
Identification of 4-(2-(4-amino-1,2,5-oxadiazol-3-yl)-1-ethyl-7-{[(3S)-3-piperidinylmethyl]oxy}-1H-imidazo[4,5-c]pyridin-4-yl)-2-methyl-3-butyn-2-ol (GSK690693), a novel inhibitor of AKT kinase. J Med Chem (2008) 1.41
In vitro and in vivo activity of novel small-molecule inhibitors targeting the pleckstrin homology domain of protein kinase B/AKT. Cancer Res (2009) 1.08
SAMPL3: blinded prediction of host-guest binding affinities, hydration free energies, and trypsin inhibitors. J Comput Aided Mol Des (2012) 1.01
Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change. J Am Chem Soc (2005) 0.93
SAMPL2 challenge: prediction of solvation energies and tautomer ratios. J Comput Aided Mol Des (2010) 0.91
Analysis of SM8 and Zap TK calculations and their geometric sensitivity. J Comput Aided Mol Des (2010) 0.88
Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK. J Comput Aided Mol Des (2014) 0.82
Aminoalkoxybenzyl pyrrolidines as novel human urotensin-II receptor antagonists. Bioorg Med Chem Lett (2005) 0.76
The application of statistical methods to cognate docking: a path forward? J Chem Inf Model (2014) 0.76