Atomic-level accuracy in simulations of large protein crystals.
York, D M, Wlodawer, A, Pedersen, L G, Darden, T A
Proper treatment of long-range Coulombic forces presents a major obstacle to providing realistic molecular dynamics simulations of macromolecules. Traditional approximations made to lessen...
Iwasaki, M, Davis, D G, Darden, T A, Pedersen, L G, Negishi, M
The mutation of Ala-117 to Val conferred dehydroepiandrosterone (DHEA) hydroxylase activity on cytochrome P-450 2a-4, with the production of both 2 alpha- and 7 alpha-hydroxyDHEA at similar rates....
An atomic model for the pleated beta-sheet structure of Abeta amyloid protofilaments.
Li, L, Darden, T A, Bartolotti, L, Kominos, D, Pedersen, L G
Synchrotron x-ray studies on amyloid fibrils have suggested that the stacked pleated beta-sheets are twisted so that a repeating unit of 24 beta-strands forms a helical turn around the fibril axis (....
Perera, L, Darden, T A, Pedersen, L G
The crystallographic structure of human coagulation factor VIIa/tissue factor complex bound with calcium ions was used to model the solution structure of the light chain of factor VIIa (residues...
Bevan, D R, Li, L, Pedersen, L G, Darden, T A
Molecular dynamics (MD) simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure. Two crystal simulations were carried out; one consisted...
Gorokhov, A, Perera, L, Darden, T A, Negishi, M, Pedersen, L C, Pedersen, L G
Heparan sulfate N-deacetylase/N-sulfotransferase (NDST) catalyzes the deacetylation and sulfation of N-acetyl-D-glucosamine residues of heparan sulfate, a key step in its biosynthesis. Recent...
Perera, L, Foley, C, Darden, T A, Stafford, D, Mather, T, Esmon, C T, ...
A solution structure for the complete zymogen form of human coagulation protein C is modeled. The initial core structure is based on the x-ray crystallographic structure of the gamma-carboxyglutamic...
Selected new developments in computational chemistry.
Darden, T A, Bartolotti, L, Pedersen, L G
Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules,...
York, D M, Darden, T A, Pedersen, L G, Anderson, M W
Human immunodeficiency virus type 1 protease is inhibited in vitro by zinc ions at neutral pH. The binding site of these ions is not known; however, experimental data suggest that binding may occur...
Atomic-level accuracy in simulations of large protein crystals.
York, D M, Wlodawer, A, Pedersen, L G, Darden, T A
Proper treatment of long-range Coulombic forces presents a major obstacle to providing realistic molecular dynamics simulations of macromolecules. Traditional approximations made to lessen...
Iwasaki, M, Davis, D G, Darden, T A, Pedersen, L G, Negishi, M
The mutation of Ala-117 to Val conferred dehydroepiandrosterone (DHEA) hydroxylase activity on cytochrome P-450 2a-4, with the production of both 2 alpha- and 7 alpha-hydroxyDHEA at similar rates....
An atomic model for the pleated beta-sheet structure of Abeta amyloid protofilaments.
Li, L, Darden, T A, Bartolotti, L, Kominos, D, Pedersen, L G
Synchrotron x-ray studies on amyloid fibrils have suggested that the stacked pleated beta-sheets are twisted so that a repeating unit of 24 beta-strands forms a helical turn around the fibril axis (....
Perera, L, Darden, T A, Pedersen, L G
The crystallographic structure of human coagulation factor VIIa/tissue factor complex bound with calcium ions was used to model the solution structure of the light chain of factor VIIa (residues...
Bevan, D R, Li, L, Pedersen, L G, Darden, T A
Molecular dynamics (MD) simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure. Two crystal simulations were carried out; one consisted...
Gorokhov, A, Perera, L, Darden, T A, Negishi, M, Pedersen, L C, Pedersen, L G
Heparan sulfate N-deacetylase/N-sulfotransferase (NDST) catalyzes the deacetylation and sulfation of N-acetyl-D-glucosamine residues of heparan sulfate, a key step in its biosynthesis. Recent...
Perera, L, Foley, C, Darden, T A, Stafford, D, Mather, T, Esmon, C T, ...
A solution structure for the complete zymogen form of human coagulation protein C is modeled. The initial core structure is based on the x-ray crystallographic structure of the gamma-carboxyglutamic...
Selected new developments in computational chemistry.
Darden, T A, Bartolotti, L, Pedersen, L G
Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules,...
York, D M, Darden, T A, Pedersen, L G, Anderson, M W
Human immunodeficiency virus type 1 protease is inhibited in vitro by zinc ions at neutral pH. The binding site of these ions is not known; however, experimental data suggest that binding may occur...