Published in J Mol Model on November 28, 2012
Standards-based curation of a decade-old digital repository dataset of molecular information. J Cheminform (2015) 0.98
Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package. Acta Crystallogr D Biol Crystallogr (2014) 0.96
Sparkle/PM7 Lanthanide Parameters for the Modeling of Complexes and Materials. J Chem Theory Comput (2013) 0.92
Accuracy issues involved in modeling in vivo protein structures using PM7. Proteins (2015) 0.89
Application of molecular modeling to urokinase inhibitors development. Biomed Res Int (2014) 0.88
An approach to creating a more realistic working model from a protein data bank entry. J Mol Model (2015) 0.88
Human insulin analogues modified at the B26 site reveal a hormone conformation that is undetected in the receptor complex. Acta Crystallogr D Biol Crystallogr (2014) 0.86
Identification of the first inhibitor of the GBP1:PIM1 interaction. Implications for the development of a new class of anticancer agents against paclitaxel resistant cancer cells. J Med Chem (2014) 0.85
Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations. Plant Physiol (2014) 0.85
Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev (2016) 0.84
Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters. J Chem Theory Comput (2016) 0.83
Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima. Adv Bioinformatics (2015) 0.82
A comparison of X-ray and calculated structures of the enzyme MTH1. J Mol Model (2016) 0.81
Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties. J Chem Theory Comput (2016) 0.81
Europium Luminescence: Electronic Densities and Superdelocalizabilities for a Unique Adjustment of Theoretical Intensity Parameters. Sci Rep (2015) 0.80
A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1. J Mol Model (2016) 0.80
Revealing the nature of intermolecular interaction and configurational preference of the nonpolar molecular dimers (H₂)₂, (N₂)₂, and (H₂)(N₂). J Mol Model (2013) 0.80
Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II. Bioorg Med Chem Lett (2014) 0.79
Enhanced semiempirical QM methods for biomolecular interactions. Comput Struct Biotechnol J (2015) 0.79
Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets. Mem Inst Oswaldo Cruz (2016) 0.78
Solvation of the fluorine containing anions and their lithium salts in propylene carbonate and dimethoxyethane. J Mol Model (2015) 0.78
Towards a barrier height benchmark set for biologically relevant systems. PeerJ (2016) 0.78
Prediction of radical scavenging activities of anthocyanins applying adaptive neuro-fuzzy inference system (ANFIS) with quantum chemical descriptors. Int J Mol Sci (2014) 0.78
Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches. J Chem Theory Comput (2014) 0.78
The α-Terpineol to 1,8-Cineole Cyclization Reaction of Tobacco Terpene Synthases. Plant Physiol (2016) 0.78
Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7. Adv Bioinformatics (2017) 0.77
Docking-based virtual screening of Brazilian natural compounds using the OOMT as the pharmacological target database. J Mol Model (2017) 0.76
Uncertainty of prebiotic scenarios: the case of the non-enzymatic reverse tricarboxylic acid cycle. Sci Rep (2015) 0.76
Insights into colour-tuning of chlorophyll optical response in green plants. Phys Chem Chem Phys (2015) 0.76
Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding. J Mol Graph Model (2016) 0.76
Nucleic acid reactivity: challenges for next-generation semiempirical quantum models. J Comput Chem (2015) 0.76
Catalytic mechanism of 5-chlorohydroxyhydroquinone dehydrochlorinase from the YCII superfamily of largely unknown function. J Biol Chem (2013) 0.76
A script for automated 3-dimentional structure generation and conformer search from 2- dimentional chemical drawing. Bioinformation (2013) 0.76
Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry. ACS Cent Sci (2017) 0.75
An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin. J Mol Model (2017) 0.75
Flexible 2D Crystals of Polycyclic Aromatics Stabilized by Static Distortion Waves. ACS Nano (2016) 0.75
Characterization of class III peroxidases from switchgrass. Plant Physiol (2016) 0.75
Systematic and efficient navigating potential energy surface: Data for silver doped gold clusters. Data Brief (2016) 0.75
EMPIRE: a highly parallel semiempirical molecular orbital program: 2: periodic boundary conditions. J Mol Model (2015) 0.75
Preserving π-conjugation in covalently functionalized carbon nanotubes for optoelectronic applications. Nat Commun (2017) 0.75
Investigating the Neuroprotective Effects of Turmeric Extract: Structural Interactions of β-Amyloid Peptide with Single Curcuminoids. Sci Rep (2016) 0.75
Crystal structure of (2E)-3-[4-(di-methyl-amino)-phen-yl]-1-(thio-phen-2-yl)prop-2-en-1-one. Acta Crystallogr E Crystallogr Commun (2017) 0.75
Predicting Structures of Ru-Centered Dyes: A Computational Screening Tool. J Phys Chem A (2016) 0.75
Molecular engineering of polymersome surface topology. Sci Adv (2016) 0.75
Q|R: quantum-based refinement. Acta Crystallogr D Struct Biol (2017) 0.75
Metal Ion Modeling Using Classical Mechanics. Chem Rev (2017) 0.75
Molecular Docking, Molecular Dynamics, and Structure-Activity Relationship Explorations of 14-Oxygenated N-Methylmorphinan-6-ones as Potent μ-Opioid Receptor Agonists. ACS Chem Neurosci (2017) 0.75
The interaction of heme with plakortin and a synthetic endoperoxide analogue: new insights into the heme-activated antimalarial mechanism. Sci Rep (2017) 0.75
Far-infrared spectroscopy of salt penetration into a collagen fiber scaffold. J Biol Phys (2015) 0.75
ILPC: simple chemometric tool supporting the design of ionic liquids. J Cheminform (2016) 0.75
Adaptive Neuro-Fuzzy Inference System Applied QSAR with Quantum Chemical Descriptors for Predicting Radical Scavenging Activities of Carotenoids. PLoS One (2015) 0.75
ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation. J Cheminform (2015) 0.75
Quantum chemical calculation of electron ionization mass spectra for general organic and inorganic molecules. Chem Sci (2017) 0.75
Solvation of the morpholinium cation in acetonitrile. Effect of an anion. J Mol Model (2016) 0.75
An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis. Chem Sci (2017) 0.75
Inhibition of hydroxyapatite formation in the presence of titanocene-amino acid complexes: an experimental and computational study. J Mater Sci Mater Med (2015) 0.75
Crystal structure, Hirshfeld analysis and mol-ecular docking with the vascular endothelial growth factor receptor-2 of (3Z)-5-fluoro-3-(hy-droxy-imino)-indolin-2-one. Acta Crystallogr E Crystallogr Commun (2017) 0.75
Stability of rolled-up GaAs nanotubes. J Mol Model (2017) 0.75
Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules. J Comput Chem (2017) 0.75
Quantitative Structure-Retention Relationships for Polycyclic Aromatic Hydrocarbons and their Oligoalkynyl-Substituted Derivatives. ChemistryOpen (2017) 0.75
Application of semiempirical electronic structure theory to compute the force generated by a single surface-mounted switchable rotaxane. J Mol Model (2017) 0.75
Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. J Mol Recognit (2017) 0.75
Empirical correction for PM7 band gaps of transition-metal oxides. J Mol Model (2016) 0.75
Understanding weakly coordinating anions: tetrakis(pentafluorophenyl)borate paired with inorganic and organic cations. J Mol Model (2017) 0.75
Benchmarking semiempirical and DFT methods for the interaction of thiophene and diethyl sulfide molecules with a Ti(OH)4(H2O) cluster. J Mol Model (2017) 0.75
Sodium-ion electrolytes based on ionic liquids: a role of cation-anion hydrogen bonding. J Mol Model (2016) 0.75
The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B (2002) 234.73
The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57
Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem (2006) 13.16
Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J Mol Model (2007) 5.72
RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. J Comput Chem (2006) 3.01
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys Chem Chem Phys (2006) 2.55
Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J Am Chem Soc (2004) 2.51
S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures. J Chem Theory Comput (2011) 1.76
Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation. J Mol Model (2003) 1.66
Application of the PM6 method to modeling proteins. J Mol Model (2008) 1.64
Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. J Comput Chem (2007) 1.46
Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes. J Chem Theory Comput (2009) 1.33
A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. J Chem Theory Comput (2009) 1.30
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. J Chem Theory Comput (2011) 1.28
The DBH24/08 Database and Its Use to Assess Electronic Structure Model Chemistries for Chemical Reaction Barrier Heights. J Chem Theory Comput (2009) 1.16
Application of the PM6 method to modeling the solid state. J Mol Model (2008) 1.15
Seemingly simple stereoelectronic effects in alkane isomers and the implications for Kohn-Sham density functional theory. Angew Chem Int Ed Engl (2006) 1.10
Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems. J Phys Chem B (2006) 1.05
A General Database for Main Group Thermochemistry, Kinetics, and Noncovalent Interactions - Assessment of Common and Reparameterized (meta-)GGA Density Functionals. J Chem Theory Comput (2009) 1.03
Representative Benchmark Suites for Barrier Heights of Diverse Reaction Types and Assessment of Electronic Structure Methods for Thermochemical Kinetics. J Chem Theory Comput (2007) 1.02
A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries. Chem Phys (2012) 0.85