A gene pathway enrichment method based on improved TF-IDF algorithm.

Gene pathway enrichment analysis is a widely used method to analyze whether a gene set is statistically enriched on certain biological pathway network. Current gene pathway enrichment methods commonly consider local importance of genes in pathways without considering the interactions between genes. In this paper, we propose a gene pathway enrichment method (GIGSEA) based on improved TF-IDF algorithm.

The Physiologic Activity and Mechanism of Quercetin-Like Natural Plant Flavonoids.

The term "vitamin P" is an old but interesting concept. Most substances in this category belong to the family of flavonoids. "Vitamin P" has also been used to define the activity of some flavonoids, including quercetin, myricetin, and rutin.

Proteins with Evolutionarily Hypervariable Domains are Associated with Immune Response and Better Survival of Basal-like Breast Cancer Patients.

Maltase-glucoamylase (MGAM) and MGAM2 both belong to the glycoside hydrolase family 31. MGAM, a therapeutic target for type 2 diabetes, is α-1,4-glucosidase and expressed in the intestine to catalyze starch digestion. MGAM2, however, is largely uncharacterized.

Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area.

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.

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected.

Amino Acids in Nine Ligand-Prefer Ramachandran Regions.

Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed.

An Algorithm for Protein Helix Assignment Using Helix Geometry.

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment.

An Accurate Model for Biomolecular Helices and Its Application to Helix Visualization.

Helices are the most abundant secondary structural elements in proteins and the structural forms assumed by double stranded DNAs (dsDNA). Though the mathematical expression for a helical curve is simple, none of the previous models for the biomolecular helices in either proteins or DNAs use a genuine helical curve, likely because of the complexity of fitting backbone atoms to helical curves. In this paper we model a helix as a series of different but all bona fide helical curves; each one best fits the coordinates of four consecutive backbone Cα atoms for a protein or P atoms for a DNA molecule.

A geometric clustering algorithm with applications to structural data.

An important feature of structural data, especially those from structural determination and protein-ligand docking programs, is that their distribution could be mostly uniform. Traditional clustering algorithms developed specifically for nonuniformly distributed data may not be adequate for their classification. Here we present a geometric partitional algorithm that could be applied to both uniformly and nonuniformly distributed data.