HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD

Electric-field-induced band bending on GaN: in situ effects of electron beam irradiation on time-dependent cathodoluminescence

Electron beam bombardment of GaN has been monitored by secondary electron (SE), cathodoluminescence (CL) imaging, simultaneous in situ CL, and specimen current (SC) measurements. Under extreme irradiation conditions, system perturbations, as seen by SE and time-dependent CL, are attributed to internal charge dynamics extending beyond the scanned areas. Under moderate irradiation conditions, the size of affected regions correlates with nominal scanned regions. Time-dependent CL at the near band edge (NBE) revealed complex interplay with SC, which was modeled through band bending at the Au/GaN interface. The system has shown distinctive internal electric field dynamics upon sample handling, affecting both time-dependent CL spectra and SC as well as producing contrast reversal in SE imaging, to which humidity adsorption could be contributing. The band-bending model presented here can account for both moderate irradiation and humidity effects through variations of depletion widths and Schottky barrier heights. Our findings are consistent with current models where e-beam activated VGa promotes decreased NBE intensities and CN promotes DL emissions

Rotation analysis of the B-X 0-1 bands of GaO

The 0-1 band of the B-2 Sigma(+)-X(2) Sigma(+) system of (GaO)-Ga-69-O-16 and (GaO)-Ga-71-O-16 has been measured and rotationally assigned. Principal molecular constants (T-01, B-0, B-1 , B-e , D-0, D-1 , alpha(e) ) have been obtained

New rotational analysis of the B-2 Sigma(+)-X-2 Sigma(+) bands in (GaO)-Ga-69-O-16 and (GaO)-Ga-71-O-16

In the emission spectrum of the (GaO)-O-16 molecule, the 0-0 and 1-0 bands of the B-X system have been rephotographed by means of conventional high-resolution spectroscopy. Clear resolution on the rotational structure near the band origins made it possible to perform reanalysis of the bands and derive new molecular constants characterizing (GaO)-Ga-69-O-16 and (GaO)-Ga-71-O-16 in the B(2)Sigma(+) and X(2)Sigma(+) states, (C) 1999 Academic Press