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Collect. Czech. Chem. Commun. 2008, 73, 1261-1270
doi:10.1135/cccc20081261

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

Jan Řezáča, Petr Jurečkab, Kevin E. Rileya, Jiří Černýa, Haydee Valdesa, Kristýna Pluháčkováa, Karel Berkaa, Tomáš Řezáča, Michal Pitoňáka, Jiří Vondrášeka and Pavel Hobzaa,b,*

a Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. and Center for Biomolecules and Complex Systems, 166 10 Prague 6, Czech Republic
b Department of Physical Chemistry, Palacký University, třída Svobody 26, 771 46 Olomouc, Czech Republic

CrossRef Cited-by Linking

  • Řezáč Jan, Riley Kevin E., Hobza Pavel: Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes. J  Comput Chem 2012, 33, 691. <doi:10.1002/jcc.22899>
  • Hättig Christof, Tew David P.: Pair natural orbitals in explicitly correlated second-order møller-plesset theory. Int Quant Chem 2012, n/a. <doi:10.1002/qua.24098>
  • Hobza Pavel: Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies. Acc Chem Rec 2012, 45, 663. <doi:10.1021/ar200255p>
  • Řezáč Jan, Hobza Pavel: Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. J Chem Theory and Comput 2012, 8, 141. <doi:10.1021/ct200751e>
  • Riley Kevin E., Platts James A., Řezáč Jan, Hobza Pavel, Hill J. Grant: Assessment of the Performance of MP2 and MP2 Variants for the Treatment of Noncovalent Interactions. J Phys Chem A 2012, 116, 4159. <doi:10.1021/jp211997b>
  • Mukherjee Goutam, Patra Niladri, Barua Poranjyoti, Jayaram B.: A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets. J Comput Chem 2011, 32, 893. <doi:10.1002/jcc.21671>
  • Tafipolsky Maxim, Engels Bernd: Accurate Intermolecular Potentials with Physically Grounded Electrostatics. J Chem Theory Comput 2011, 7, 1791. <doi:10.1021/ct200185h>
  • Řezáč Jan, Riley Kevin E., Hobza Pavel: S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures. J Chem Theory and Comput 2011, 7, 2427. <doi:10.1021/ct2002946>
  • Řezáč Jan, Riley Kevin E., Hobza Pavel: Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries. J Chem Theory and Comput 2011, 7, 3466. <doi:10.1021/ct200523a>
  • Steinmann Stephan N., Corminboeuf Clemence: Comprehensive Benchmarking of a Density-Dependent Dispersion Correction. J Chem Theory and Comput 2011, 7, 3567. <doi:10.1021/ct200602x>
  • Riley Kevin E., Řezáč Jan, Hobza Pavel: MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets. PCCP 2011, 13, 21121. <doi:10.1039/c1cp22525a>
  • Steber Amanda L., Neill Justin L., Zaleski Daniel P., Pate Brooks H., Lesarri Alberto, Bird Ryan G., Vaquero-Vara Vanesa, Pratt David W.: Structural studies of biomolecules in the gas phase by chirped-pulse Fourier transform microwave spectroscopy. Faraday Disc 2011, 150, 227. <doi:10.1039/c1fd00008j>
  • Hobza Pavel: The calculation of intermolecular interaction energies. Annu Rep Prog Chem Sect C 2011, 107, 148. <doi:10.1039/c1pc90005f>
  • Burns Lori A., Mayagoitia Álvaro Vázquez-, Sumpter Bobby G., Sherrill C. David: Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals. J Chem Phys 2011, 134, 084107. <doi:10.1063/1.3545971>
  • Andrinopoulos Lampros, Hine Nicholas D. M., Mostofi Arash A.: Calculating dispersion interactions using maximally localized Wannier functions. Journal Chemical Physics 2011, 135, 154105. <doi:10.1063/1.3647912>
  • Adams Sam, de Castro Pablo, Echenique Pablo, Estrada Jorge, Hanwell Marcus D, Murray-Rust Peter, Sherwood Paul, Thomas Jens, Townsend Joe: The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age. J Cheminform 2011, 3, 38. <doi:10.1186/1758-2946-3-38>
  • Kolář Michal, Berka Karel, Jurečka Petr, Hobza Pavel: On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes. Chem Eur J of Chem Phys 2010, 11, 2399. <doi:10.1002/cphc.201000109>
  • Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Mochizuki Yuji, Watanabe Hirofumi, Tanaka Shigenori, Xia Wen Wen, Yao Li, Chen Baojiu, Wang Donglai, Zhao Caihong, Xin Guang, Hou Dongyan: Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)���RNA complex system. Journal of Molecular Structure: THEOCHEM 2010, 962, 45. <doi:10.1016/j.theochem.2010.09.013>
  • Podeszwa Rafał, Patkowski Konrad, Szalewicz Krzysztof: Improved interaction energy benchmarks for dimers of biological relevance. Phys Chem Chem Phys 2010, 12, 5974. <doi:10.1039/b926808a>
  • Watanabe Hirofumi, Tanaka Shigenori: Fragment Molecular Orbital Method: Application to Protein-Ligand Binding. Interdisciplinary Bio Central 2010, 2, 6.1. <doi:10.4051/ibc.2010.2.2.0006>
  • Pitoňák Michal, Neogrády Pavel, Černý Jiří, Grimme Stefan, Hobza Pavel: Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data. Chem Eur J of Chem Phys 2009, 10, 282. <doi:10.1002/cphc.200800718>