Kernel energy method applied to vesicular stomatitis virus nucleoprotein

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 6, 2009, Pages 1731-1736

  Huang, Lulu ^a   Massa, Lou ^b   Karle, Jerome ^a  

^a NAVAL RESEARCH LABORATORY   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Hartree Fock; KEM; M ller Plesset; Quantum mechanics

Indexed keywords

HYDROGEN; VIRUS NUCLEOPROTEIN;

ARTICLE; COMPUTER PROGRAM; ENERGY; HYDROGEN BOND; KERNEL METHOD; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THEORY; VESICULAR STOMATITIS VIRUS;

HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEOPROTEINS; QUANTUM THEORY; SOFTWARE; VESICULOVIRUS; VIRAL PROTEINS;

VESICULAR STOMATITIS VIRUS;

EID: 60549087701     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0811959106     Document Type: Article

References (19)

1. Zhang X, Green T-J, Tsao J, Qiu S, Luo M (2008) Role of intermolecular interactions of vesicular stomatitis virus nucleoprotein in RNA encapsidation. J Virol 82:674-682.
2. Huang L, Massa L, Karle J (2005) Kernel energy method illustrated with peptides. Int J Quantum Chem 103:808-817.
3. Huang L, Massa L, Karle J (2006) The kernel energy method: Basis functions and quantum methods. Int J Quantum Chem 106:447-457.
4. Huang L, Massa L, Karle J (2005) Kernel energy method: Application to insulin. PNAS 102:2690-12693.
5. Huang L, Massa L, Karle J (2005) Kernel energy method: Application to DNA. Biochemistry 44:16747-16752.
6. Huang L, Massa L, Karle J (2006) Kernel energy method: Application to a tRNA. PNAS 103:1233-1237.
7. Huang L, Massa L, Karle J (2007) Drug-Target interaction energies by the kernel energy method: Aminoglycoside drugs and ribosomal A-site RNA target. PNAS 104:4261-4266.
8. Huang L, Massa L, Karle J (2007) Kernel energy method: The interaction energy of the collagen triple helix. J Chem Theory Comput 3:1337-1341.
9. Hehre W-J, Stewart R-F, Pople J-A (1969) Seld-consistent molecular-orbital methods. I. Use of Gaussian expansions of Slater-type atonic orbitals. J Chem Phys 51:2657-2664.
10. Roothaan C-C-J (1951) New developments in molecular orbital theory. Rev Mol Phys 23:69-89.
11. Pople J-A, Nesbet R-K (1954) Self-consistent orbitals for radicals. J Chem Phys 22:571-572.
12. Tiwari A, Panigrahi S-K (2007) HBAT: Hydrogen bond analysis tool (HBAT 1.0), In Silico Biology 7:0057.
13. Ditchfield R, Hehre W-J, Pople J-A (1971) Self-consistent molecular-orbital Methods. IX. An extended Gaussian-type basis for molecular-orbital of organic molecules. J Chem Phys 54:724-728.
14. Francl M-M, et al. (1982) Self-consistent molecular orbital Methods. XXIII. A polarization-type basis set for second-row elements. J Chem Phys 77:3654-3665.
15. Rassolov V-A, Ratner M-A, Pople J-A, Redfern P-C, Curtiss L-A (2001) 6-31G* basis set for third-row atoms. J Comp Chem 22:976-984.
16. Petersson G-A, Bennett A, Tensfeldt T-G, Al-Laham M-A, Shirley W-A, Mantzaris J (1988) A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements. J Chem Phys 89:2193-2218.
17. Møller C, Plesset M-S (1934) Note on an approximation treatment for many-electron systems. Phys Rev 46:618-622.
18. Head-Gordon M, Pople J-A, Frisch M-J (1988) MP2 energy evaluation by direct methods. Chem Phys Lett 153:503-506.
19. Saebø S-A (1989) Avoiding the integral storage bottleneck in LCAO calculations of electron correlation. J Chem Phys Lett 154:83-89.