Accuracy issues involved in modeling in vivo protein structures using PM7
暂无分享,去创建一个
James J. P. Stewart | J. Stewart | Sonja B. Braun-Sand | Benjamin P. Martin | Christopher J. Brandon | Sonja B. Braun‐Sand
[1] M. Head‐Gordon,et al. A fifth-order perturbation comparison of electron correlation theories , 1989 .
[2] Jack Snoeyink,et al. Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .
[3] A. Klamt,et al. COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .
[4] S. Grimme,et al. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.
[5] Marvin Edelman,et al. The limit of accuracy of protein modeling: influence of crystal packing on protein structure. , 2005, Journal of molecular biology.
[6] Alfredo Mayall Simas,et al. RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I , 2006, J. Comput. Chem..
[7] Vincent B. Chen,et al. Correspondence e-mail: , 2000 .
[8] Pavel Hobza,et al. S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures , 2011, Journal of chemical theory and computation.
[9] James J. P. Stewart,et al. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters , 2012, Journal of Molecular Modeling.
[10] Karel Berka,et al. Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples , 2008 .
[11] M. Plesset,et al. Note on an Approximation Treatment for Many-Electron Systems , 1934 .
[12] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[13] Jirí Cerný,et al. 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. , 2006, Physical chemistry chemical physics : PCCP.
[14] James J. P. Stewart,et al. Application of the PM6 method to modeling proteins , 2009, Journal of molecular modeling.
[15] Martin Korth,et al. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields , 2010 .
[16] J. Stewart. Optimization of parameters for semiempirical methods I. Method , 1989 .
[17] Michal Otyepka,et al. Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors , 2011, J. Comput. Aided Mol. Des..
[18] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[19] J. Stewart. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.