Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic ne...

Background: Diabetes mellitus (DM) type 2 is a metabolic disorder that needs special attention because it can damage several organs if the severity increases. One of treatments for diabetes by inhibiting Dipeptidyl peptidase 4 (DPP-IV) with vildagliptin to prolong hypoglycemic effect GLP-1 and GIP. Objective: In search candidate compounds as new antidiabetic compounds, an in silico test molecul...

PURPOSE The purpose of this prospective multicenter study was to assess the accuracy of a computer-aided surgical simulation (CASS) protocol for orthognathic surgery. MATERIALS AND METHODS The accuracy of the CASS protocol was assessed by comparing planned outcomes with postoperative outcomes of 65 consecutive patients enrolled from 3 centers. Computer-generated surgical splints were used for...

In this paper, the variation of the values of dihedral angles in proteins is divided into two categories by analyzing distributions in a database of structures determined at a resolution of 1.8 A or better [Lovell et al. (2003), Proteins Struct. Funct. Genet. 50, 437-450]. The first analysis uses the torsion angle for the Calpha-Cbeta bond (chi1) of all Gln, Glu, Arg and Lys residues ('unbranch...

The role of benzodiazepine derivatives (BZD) as a privileged scaffold that mimics beta-turn structures (Ripka et al. (1993) Tetrahedron 49:3593-3608) in peptide/protein recognition was reexamined in detail. Stable BZD ring conformers were determined with MM3, and experimental reverse-turn structures were extracted from the basis set of protein crystal structures previously defined by Ripka et a...

The Community Structure-Activity Resource (CSAR) recently held its first blinded exercise based on data provided by Abbott, Vertex, and colleagues at the University of Michigan, Ann Arbor. A total of 20 research groups submitted results for the benchmark exercise where the goal was to compare different improvements for pose prediction, enrichment, and relative ranking of congeneric series of co...

Similarity of protein structures has been analyzed using three-dimensional Delaunay triangulation patterns derived from the backbone representation. It has been found that structurally related proteins have a common spatial invariant part, a set of tetrahedrons, mathematically described as a common spatial subgraph volume of the three-dimensional contact graph derived from Delaunay tessellation...

Evaporation coefficient (KE) is defined as the ratio of actual evaporation over potential evaporation under the same atmospheric conditions. The use of KE provides an alternative means for evaluating soil moisture status and quantifying soil evaporation by reducing in situ measurements. However, little effort has been made to evaluate the estimation of KE over soil surfaces. In this study, a re...

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estima...

The purpose of this study was to evaluate adaptive daily planning for cervi-cal cancer patients who underwent high-dose-rate intracavitary brachytherapy (HDR-BT) using comprehensive interfractional organ motion measurements. This study included 22 cervical cancer patients who underwent 5 fractions of HDR-BT. Regions of interest (ROIs) including high-risk clinical tumor volume (HR-CTV) and organ...