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Trial Calculations (trial + calculation)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

WATGEN: An algorithm for modeling water networks at protein,protein interfaces

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2007
Huynh-Hoa Bui
Abstract Water molecules at protein,protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein,protein or protein,peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein,peptide interfaces (X-ray resolutions , 2.0 Å), using different criteria for water placement. The energies of the predicted water networks were evaluated in AMBER8 and used in the choice of parameters for WATGEN. The 126 interfaces include 1264 experimentally determined bridging water sites, and the WATGEN algorithm predicts 72 and 88% of these sites within 1.5 and 2.0 Å, respectively. The predicted number of water molecules at each interface was much higher than the number of water molecules identified experimentally. Therefore, random placement of the same number of water molecules as that predicted at each interface was performed as a control, and resulted in only 22 and 40% of water sites placed within 1.5 and 2.0 Å of experimental sites, respectively. Based on these data, we conclude that WATGEN can accurately predict the location of water molecules at a protein,peptide interface, and this may be of value for understanding the energetics and specificity of biomolecular association. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source]

Retrieving low- and medium-resolution structural features of macromolecules directly from the diffraction intensities , a real-space approach to the X-ray phase problem

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2008
Wu-Pei Su
A simple mathematical algorithm is proposed to generate electron-density functions whose Fourier amplitudes match the diffraction intensities. The function is by construction everywhere positive. Using appropriate averaging procedures, the high-density regions of such functions could yield important structural information about macromolecular crystals. Trial calculations on protein crystals show that the protein envelope plus other structural motifs such as barrels and secondary structures could be recognized in the density maps. As such, the algorithm could provide a basis for new phasing methods or supplement existing phasing methods. [source]

A modified X,,,Y method

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2001
Yan Chen
The X,,,Y method seeks to solve the unknown phases of the X-ray reflections by minimizing a function (the X,,,Y function) of the phases. This cost function has been supplemented with a residual term. The total cost function is minimized by varying the positions of atoms. Simulated annealing is used to implement the minimization. Trial calculations for structures containing up to 176 non-H equal atoms have been carried out successfully. [source]

Computation and analysis of 19F substituent chemical shifts of some bridgehead-substituted polycyclic alkyl fluorides

MAGNETIC RESONANCE IN CHEMISTRY, Issue 7 2003
William Adcock
Abstract The 19F NMR shieldings for several remotely substituted rigid polycyclic alkyl fluorides with common sets of substituents covering a wide range of electronic effects were calculated using the DFT-GIAO theoretical model. The level of theory, B3LYP/6,311+G(2d,p), was chosen based on trial calculations which gave good agreement with experimental values where known. The optimized geometries were used to obtain various molecular parameters (fluorine natural charges, electron occupancies on fluorine of lone pairs and of the CF bond, and hybridization states) by means of natural bond orbital (NBO) analysis which could help in understanding electronic transmission mechanisms underlying 19F substituent chemical shifts (SCS) in these systems. Linear regression analysis was employed to explore the relationship between the calculated 19F SCS and polar substituent constants and also the NBO derived molecular parameters. The 19F SCS are best described by an electronegativity parameter. The most pertinent molecular parameters appear to be the occupation number of the NBO p-type fluorine lone pair and the occupation number of the CF antibonding orbital. This trend suggests that in these types of rigid saturated systems hyperconjugative interactions play a key role in determining the 19F SCS. Electrostatic field effects appear to be relatively unimportant. Copyright © 2003 John Wiley & Sons, Ltd. [source]