The effectiveness of Intensity Modulated Radiation Therapy (IMRT) is 9 compromised by involuntary motion (e.g. respiration, cardiac activity). The feasibility 10 of processing ultrasound echo data to automatically estimate 3D liver motion for real11 time IMRT guidance was previously demonstrated, but performance was limited by an 12 acquisition speed of 2 volumes per second due to hardware rest...

Statistical energy functions are discrete (or stepwise) energy functions that lack van der Waals repulsion. As a result, they are often applied directly to a given structure (native or decoy) without further energy minimization being performed to the structure. However, the full benefit (or hidden defect) of an energy function cannot be revealed without energy minimization. This paper tests a r...

G-Protein Coupled Receptors (GPCRs) are a big family of eukaryotic cell transmembrane proteins, responsible for numerous biological processes. From practical viewpoint around 34% the drugs approved by US Food and Drug Administration target these receptors. They can be analyzed from their simulated molecular dynamics, including prediction behavior in presence drugs. In this paper, capability Lon...

Vat photopolymerization (VPP) presents new opportunities for metals to achieve the design freedom of components. However, material properties copper powder and inherent defects technology seriously hinder its application in high-precision metal additive manufacturing. Precision control is key obtaining minimal precision parts when prepared by reduction photopolymerization. This paper employed v...

MOTIVATION Even the best sequence alignment methods frequently fail to correctly identify the framework regions for which backbones can be copied from the template into the target structure. Since the underprediction and, more significantly, the overprediction of these regions reduces the quality of the final model, it is of prime importance to attain as much as possible of the true structural ...

Density functional theory (DFT) is the only quantum-chemical avenue for calculating thermochemical/kinetic properties of large polycyclic aromatic hydrocarbons (PAHs) such as graphene nanoflakes. Using CCSD(T)/CBS PAH isomerization energies, we find that all generalized gradient approximation (GGA) and meta GGA DFT functionals have severe difficulties in describing isomerization energies in PAH...

The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove binders distamycin and pentamidine. Autodock and Surflex dock daunorubicin and distamycin to their nuclei...

Simulaid performs a large number of simulation-related tasks: interconversion and modification of structure and trajectory files, optimization of orientation, and a large variety of analysis functions. The program can handle structures in PDB (Berman et al., Nucleic Acids Res 2000, 28, 235), Charmm (Brooks et al., J Comput Chem 4, 187) CRD, Amber (Case et al.), Macromodel (Mohamadi et al., J Co...

The co-crystal of HA X-31 and a promising small molecule inhibitor, tert-butyl hydroquinone (TBHQ) 1 , was solved back in 2008 (PDBID: 3EYM) 8. Visual inspection of the 3EYM's TBHQ binding pocket via Chimera 7 reaffirmed TBHQ's drug-like potential and the interactions noted in Russel et al. The structural differences between Group 1 and Group 2 HA were confirmed using the matchmaker function pr...