BACKGROUND AND OBJECTIVE Aggressive periodontitis (AgP) is a specific type of periodontal disease that is characterized by rapid attachment loss and bone destruction. While attempting to identify genetic polymorphisms associated with AgP, previous research has focused on candidate genes that may be involved in immune responses to microbial infections. In this study, the focus was on single nucl...

The bone remodeling and homeostasis are mainly controlled by the receptor-activator of nuclear factor kB (RANK), its ligand RANKL, and the soluble decoy receptor osteoprotegerin (OPG) pathway. While there is a strong association between osteoporosis and skeletal muscle dysfunction, the functional relevance of a particular biological pathway that synchronously regulates bone and skeletal muscle ...

In this paper we study the structure of standard Einstein solvmanifolds of arbitrary rank. Also the validity of a variational method for finding standard Einstein solvmanifolds is proved.

Simplified model binding sites allow one to isolate entangled terms in molecular energy functions. Here, we investigate the effects on ligand recognition of the introduction of a histidine into a hydrophobic cavity in lysozyme. We docked 656040 molecules and tested 26 highly and nine poorly ranked. Twenty-one highly ranked molecules bound and five were false positives, while three poorly ranked...

The Protein Data Bank (PDB) has been processed to extract a screening protein library (sc-PDB) of 2148 entries. A knowledge-based detection algorithm has been applied to 18,000 PDB files to find regular expressions corresponding to either protein, ions, co-factors, solvent, or ligand atoms. The sc-PDB database comprises high-resolution X-ray structures of proteins for which (i) a well-defined a...

Docking is a computational technique that samples conformations of small molecules in protein binding sites; scoring functions are used to assess which of these conformations best complements the protein binding site. An evaluation of 10 docking programs and 37 scoring functions was conducted against eight proteins of seven protein types for three tasks: binding mode prediction, virtual screeni...

Four of the most well-known, commercially available docking programs, FlexX, GOLD, GLIDE, and ICM, have been examined for their ligand-docking and virtual-screening capabilities. The relative performance of the programs in reproducing the native ligand conformation from starting SMILES strings for 164 high-resolution protein-ligand complexes is presented and compared. Applying only the native s...

The relative ligand donor strengths of 10 pyrazole-derived ligands has been determined with great accuracy, making use of the interdependence between the donor strength of the co-ligand and the (13)C NMR chemical shift of the (i)Pr(2)-bimy carbene signal in trans-[PdBr(2)((i)Pr(2)-bimy)L] complexes ((i)Pr(2)-bimy = 1,3-diisopropylbenzimidazolin-2-ylidene; L = pyrazole-derived ligand). Even subt...

Protein ligand-binding site prediction is highly important for protein function determination and structure-based drug design. Over the past twenty years, dozens of computational methods have been developed to address this problem. Soga et al. identified ligand cavities based on the preferences of amino acids for the ligand-binding site (RA) and proposed the propensity for ligand binding (PLB) ...