Quantum mechanics simulation of protein dynamics on long timescale

Proteins: Structure, Function and Genetics

Volumn 44, Issue 4, 2001, Pages 484-489

  Liu, Haiyan ^a,b,e   Elstner, Marcus ^c,d   Kaxiras, Efthimios ^c   Frauenheim, Thomas ^d   Hermans, Jan ^b   Yang, Weitao ^a  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c HARVARD UNIVERSITY   (United States)

^d UNIVERSITY OF PADERBORN   (Germany)

^e UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Molecular dynamics simulation; Protein structure; Quantum mechanics; Structural accuracy

Indexed keywords

CRAMBIN; PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; DYNAMICS; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; QUANTUM MECHANICS; SIMULATION;

ALANINE; BIOMECHANICS; COMPUTER SIMULATION; ELECTROSTATICS; OLIGOPEPTIDES; PLANT PROTEINS; PROTEIN CONFORMATION; QUANTUM THEORY; THERMODYNAMICS; TIME FACTORS; WATER;

EID: 0035451906     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1114     Document Type: Article

References (27)

1. Protein structural fluctuations during a period of 100 ps
2. Pathways to a protein folding intermediate observed in a 1- microsecond simulation in aqueous solution
3. Peptide folding: When simulation meets experiment
4. Theoretic studies of enzymic reactions: Dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
5. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
6. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
7. A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules
8. Direct calculation of electron density in density-functional theory
9. Self-consistent-charge-density-functional tight-binding method for simulations of complex materials properties
10. A self-consistent charge density-functional based tight-binding scheme for large biomolecules
11. A second generation force field for the simulation of proteins, nucleic acids and organic molecules
12. A consistent empirical potential for water-protein interactions
13. Energy minimizations of rubredoxin
14. All-atom empirical potential for molecular modeling and dynamics studies of proteins
15. Accurate protein crystallography at ultra-high resolution: Valence electron distribution in crambin
16. Comparison of simple potential functions for simulating liquid water
17. Atoms, molecules, solids and surfaces: Applications of the generalized gradient approximation for exchange and correlation
18. Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon
19. Application of an approximate density-functional method to sulfur-containing compounds
20. The high resolution (0.83 Å) crystal structure of the hydrophobic protein crambin at 130 K
21. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
22. On searching neighbours in computer simulations of macromolecular systems
23. Transferable ab initio intermolecular potentials. 1. Derivation from methanol dimer and trimer calculations
24. Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems
25. Ab initio geometry determinations in proteins. 1. Crambin
26. Charge-transfer interactions in macromolecular systems: A new view of the protein/water interface
27. Energy minimization for tertiary structure prediction of homologous proteins-a-1-purothionin and viscotoxin-A3 models from crambin